rs2497938

Variant names:

• chrX-67343176-T-C
• rs2497938

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.359 in 110,144 control chromosomes in the GnomAD database, including 9,190 homozygotes. There are 10,807 hemizygotes in GnomAD. 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 0.36 (9190 hom., 10807 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.359 AC: 39530 AN: 110086 Hom.: 9182 Cov.: 22

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000857

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.359 AC: 39594 AN: 110144 Hom.: 9190 Cov.: 22 AF XY: 0.333 AC XY: 10807 AN XY: 32428

African (AFR) AF: 0.863 AC: 25939 AN: 30068

American (AMR) AF: 0.175 AC: 1813 AN: 10336

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 272 AN: 2634

East Asian (EAS) AF: 0.000860 AC: 3 AN: 3489

South Asian (SAS) AF: 0.0782 AC: 205 AN: 2621

European-Finnish (FIN) AF: 0.179 AC: 1038 AN: 5813

Middle Eastern (MID) AF: 0.256 AC: 55 AN: 215

European-Non Finnish (NFE) AF: 0.184 AC: 9721 AN: 52788

Other (OTH) AF: 0.310 AC: 465 AN: 1501

Alfa AF: 0.248 Hom.: 19374

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2497938; hg19: chrX-66563018;