chrX-152846330-A-G

Variant names:

• chrX-152846330-A-G
• NM_015922.3:c.6A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6 BP7

The NM_015922.3(NSDHL):​c.6A>G​(p.Glu2Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 24)
• Consequence: NSDHL NM_015922.3 synonymous
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.555
• Publications: 0 publications found

Genes affected

NSDHL (HGNC:13398): (NAD(P) dependent steroid dehydrogenase-like) The protein encoded by this gene is localized in the endoplasmic reticulum and is involved in cholesterol biosynthesis. Mutations in this gene are associated with CHILD syndrome, which is a X-linked dominant disorder of lipid metabolism with disturbed cholesterol biosynthesis, and typically lethal in males. Alternatively spliced transcript variants with differing 5' UTR have been found for this gene. [provided by RefSeq, Jul 2008]

NSDHL Gene-Disease associations (from GenCC):

• CHILD syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet, G2P
• CK syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant X-152846330-A-G is Benign according to our data. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-152846330-A-G is described in CliVar as Likely_benign. Clinvar id is 3044975.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=-0.555 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSDHL	NM_015922.3	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 2 of 8	ENST00000370274.8	NP_057006.1
NSDHL	NM_001129765.2	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 3 of 9		NP_001123237.1
NSDHL	NM_001441099.1	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 4 of 10		NP_001428028.1
NSDHL	XM_017029564.2	c.54A>G	p.Glu18Glu	synonymous_variant	Exon 2 of 8		XP_016885053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSDHL	ENST00000370274.8	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 2 of 8	1	NM_015922.3	ENSP00000359297.3
NSDHL	ENST00000440023.5	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 3 of 9	5		ENSP00000391854.1
NSDHL	ENST00000432467.1	c.6A>G	p.Glu2Glu	synonymous_variant	Exon 3 of 8	3		ENSP00000396266.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 24

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

NSDHL-related disorder Benign:1

Feb 04, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.36
DANN	Benign	0.52
PhyloP100		-0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

hg19: chrX-152014874;