rs7065976

Variant names:

• chrX-149231514-T-A
• rs7065976

Your query was ambiguous. Multiple possible variants found:

• chrX-149231514-T-A
• chrX-149231514-T-G

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 0.567 in 110,900 control chromosomes in the GnomAD database, including 15,655 homozygotes. There are 18,767 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 0.57 (15655 hom., 18767 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.567 AC: 62885 AN: 110842 Hom.: 15670 Cov.: 23

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.567 AC: 62857 AN: 110900 Hom.: 15655 Cov.: 23 AF XY: 0.566 AC XY: 18767 AN XY: 33134

African (AFR) AF: 0.125 AC: 3836 AN: 30766

American (AMR) AF: 0.625 AC: 6499 AN: 10406

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2002 AN: 2634

East Asian (EAS) AF: 0.836 AC: 2914 AN: 3487

South Asian (SAS) AF: 0.644 AC: 1660 AN: 2578

European-Finnish (FIN) AF: 0.729 AC: 4250 AN: 5833

Middle Eastern (MID) AF: 0.681 AC: 147 AN: 216

European-Non Finnish (NFE) AF: 0.762 AC: 40218 AN: 52812

Other (OTH) AF: 0.612 AC: 918 AN: 1499

Alfa AF: 0.650 Hom.: 5310

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.73
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7065976; hg19: chrX-148313044;