rs961747

Variant names:

• chrX-33618320-A-G
• rs961747

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 0.118 in 111,016 control chromosomes in the GnomAD database, including 1,198 homozygotes. There are 3,848 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 0.12 (1198 hom., 3848 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 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: 0.118 AC: 13106 AN: 110962 Hom.: 1199 Cov.: 23

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0664

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.118 AC: 13125 AN: 111016 Hom.: 1198 Cov.: 23 AF XY: 0.115 AC XY: 3848 AN XY: 33378

African (AFR) AF: 0.274 AC: 8376 AN: 30560

American (AMR) AF: 0.185 AC: 1922 AN: 10372

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 74 AN: 2628

East Asian (EAS) AF: 0.382 AC: 1322 AN: 3463

South Asian (SAS) AF: 0.184 AC: 496 AN: 2695

European-Finnish (FIN) AF: 0.0299 AC: 180 AN: 6025

Middle Eastern (MID) AF: 0.0732 AC: 15 AN: 205

European-Non Finnish (NFE) AF: 0.0103 AC: 543 AN: 52871

Other (OTH) AF: 0.130 AC: 197 AN: 1511

Alfa AF: 0.0760 Hom.: 414

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.055
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs961747; hg19: chrX-33636437;