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. The variant received -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
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -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

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

African (AFR) AF: 0.296 AC: 8981 AN: 30328

American (AMR) AF: 0.759 AC: 7778 AN: 10249

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 2494 AN: 2608

East Asian (EAS) AF: 0.599 AC: 2081 AN: 3477

South Asian (SAS) AF: 0.772 AC: 1964 AN: 2545

European-Finnish (FIN) AF: 0.899 AC: 5135 AN: 5709

Middle Eastern (MID) AF: 0.888 AC: 191 AN: 215

European-Non Finnish (NFE) AF: 0.896 AC: 47305 AN: 52771

Other (OTH) AF: 0.766 AC: 1144 AN: 1494

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
PhyloP100		-0.098

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

dbSNP: rs7471388; hg19: chrX-71161082;