rs3761581

Positions:

• chrX-129655744-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 0.108 in 111,718 control chromosomes in the GnomAD database, including 1,043 homozygotes. There are 3,534 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 0.11 (1043 hom., 3534 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12082 AN: 111665 Hom.: 1043 Cov.: 23 AF XY: 0.104 AC XY: 3524 AN XY: 33929

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.00416

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0466

Gnomad NFE AF: 0.0221

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.108 AC: 12092 AN: 111718 Hom.: 1043 Cov.: 23 AF XY: 0.104 AC XY: 3534 AN XY: 33992

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.0684

Gnomad4 ASJ AF: 0.00416

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0221

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.0352 Hom.: 2410

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761581; hg19: chrX-128789721;