rs1931662

chrX-121730843-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 36087 AN: 110228 Hom.: 4479 Cov.: 23 AF XY: 0.307 AC XY: 10018 AN XY: 32654

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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.360

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931662; hg19: chrX-120864696;