chrX-96017659-T-G

Variant names:

• chrX-96017659-T-G
• rs2761647

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 0.151 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 16513 AN: 109226 Hom.: 1202 Cov.: 21

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

African (AFR) AF: 0.272 AC: 8174 AN: 30006

American (AMR) AF: 0.200 AC: 2040 AN: 10178

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 205 AN: 2616

East Asian (EAS) AF: 0.00290 AC: 10 AN: 3446

South Asian (SAS) AF: 0.0591 AC: 153 AN: 2591

European-Finnish (FIN) AF: 0.0718 AC: 406 AN: 5651

Middle Eastern (MID) AF: 0.0810 AC: 17 AN: 210

European-Non Finnish (NFE) AF: 0.101 AC: 5318 AN: 52416

Other (OTH) AF: 0.134 AC: 196 AN: 1464

Alfa AF: 0.121 Hom.: 3547

Bravo AF: 0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2761647; hg19: chrX-95272658;