X-71941232-C-G

Variant names:

• chrX-71941232-C-G
• rs7471388
• NM_001013627.3:c.280+29865C>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001013627.3(NHSL2):​c.280+29865C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.71 (22089 hom., 22921 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NHSL2 NM_001013627.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

NHSL2 (HGNC:33737): (NHS like 2) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NHSL2	NM_001013627.3	c.280+29865C>G		intron_variant	Intron 1 of 7	ENST00000633930.2	NP_001013649.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NHSL2	ENST00000633930.2	c.280+29865C>G		intron_variant	Intron 1 of 7	5	NM_001013627.3	ENSP00000488668.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 77680 AN: 110018 Hom.: 22091 Cov.: 22 AF XY: 0.710 AC XY: 22896 AN XY: 32234

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.761

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.706 AC: 77694 AN: 110074 Hom.: 22089 Cov.: 22 AF XY: 0.710 AC XY: 22921 AN XY: 32300

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.766

Alfa AF: 0.663 Hom.: 2857

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.84
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs7471388; hg19: chrX-71161082;