rs7065976

Positions:

• chrX-149231514-T-A
• chrX-149231514-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 0.567 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.567 AC: 62885 AN: 110842 Hom.: 15670 Cov.: 23 AF XY: 0.567 AC XY: 18763 AN XY: 33068

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.612

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7065976; hg19: chrX-148313044;