rs3761581

Variant names:

• chrX-129655744-A-C
• rs3761581

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 0.108 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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12082 AN: 111665 Hom.: 1043 Cov.: 23

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

African (AFR) AF: 0.272 AC: 8312 AN: 30601

American (AMR) AF: 0.0684 AC: 730 AN: 10670

Ashkenazi Jewish (ASJ) AF: 0.00416 AC: 11 AN: 2643

East Asian (EAS) AF: 0.377 AC: 1316 AN: 3495

South Asian (SAS) AF: 0.121 AC: 326 AN: 2691

European-Finnish (FIN) AF: 0.0113 AC: 69 AN: 6117

Middle Eastern (MID) AF: 0.0419 AC: 9 AN: 215

European-Non Finnish (NFE) AF: 0.0221 AC: 1175 AN: 53086

Other (OTH) AF: 0.0948 AC: 144 AN: 1519

Alfa AF: 0.0503 Hom.: 4501

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3761581; hg19: chrX-128789721;