chrX-149231514-T-A

Variant names:

• chrX-149231514-T-A
• rs7065976

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 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 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;