rs1931662

Variant names:

• chrX-121730843-A-C
• rs1931662

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 0.327 in 110,283 control chromosomes in the GnomAD database, including 4,483 homozygotes. There are 10,031 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 0.33 (4483 hom., 10031 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.371 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: 0.327 AC: 36087 AN: 110228 Hom.: 4479 Cov.: 23

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 36095 AN: 110283 Hom.: 4483 Cov.: 23 AF XY: 0.307 AC XY: 10031 AN XY: 32719

African (AFR) AF: 0.313 AC: 9558 AN: 30545

American (AMR) AF: 0.287 AC: 2962 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1182 AN: 2620

East Asian (EAS) AF: 0.389 AC: 1344 AN: 3458

South Asian (SAS) AF: 0.292 AC: 774 AN: 2654

European-Finnish (FIN) AF: 0.258 AC: 1504 AN: 5828

Middle Eastern (MID) AF: 0.462 AC: 97 AN: 210

European-Non Finnish (NFE) AF: 0.341 AC: 17883 AN: 52470

Other (OTH) AF: 0.360 AC: 545 AN: 1513

Alfa AF: 0.340 Hom.: 2804

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.67
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1931662; hg19: chrX-120864696;