rs2761647

chrX-96017659-T-G

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 0.151 in 109,258 control chromosomes in the GnomAD database, including 1,203 homozygotes. There are 4,521 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 0.15 (1203 hom., 4521 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.151 AC: 16513 AN: 109226 Hom.: 1202 Cov.: 21 AF XY: 0.142 AC XY: 4513 AN XY: 31760

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0118

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0776

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 16527 AN: 109258 Hom.: 1203 Cov.: 21 AF XY: 0.142 AC XY: 4521 AN XY: 31802

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.134

Alfa AF: 0.109 Hom.: 2148

Bravo AF: 0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2761647; hg19: chrX-95272658;