rs10521401

chrX-95657652-A-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 0.095 in 112,016 control chromosomes in the GnomAD database, including 970 homozygotes. There are 2,861 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 0.095 (970 hom., 2861 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.0947 AC: 10601 AN: 111957 Hom.: 966 Cov.: 23 AF XY: 0.0829 AC XY: 2831 AN XY: 34163

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00366

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0297

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0950 AC: 10643 AN: 112016 Hom.: 970 Cov.: 23 AF XY: 0.0836 AC XY: 2861 AN XY: 34232

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0493

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00367

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0211

Gnomad4 OTH AF: 0.0727

Alfa AF: 0.0648 Hom.: 320

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521401; hg19: chrX-94912651;