X-95657652-A-G

Variant names:

• chrX-95657652-A-G
• rs10521401

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 0.095 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 10601 AN: 111957 Hom.: 966 Cov.: 23

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

African (AFR) AF: 0.286 AC: 8762 AN: 30610

American (AMR) AF: 0.0493 AC: 522 AN: 10587

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 39 AN: 2646

East Asian (EAS) AF: 0.00 AC: 0 AN: 3583

South Asian (SAS) AF: 0.00367 AC: 10 AN: 2726

European-Finnish (FIN) AF: 0.0112 AC: 69 AN: 6187

Middle Eastern (MID) AF: 0.0326 AC: 7 AN: 215

European-Non Finnish (NFE) AF: 0.0211 AC: 1121 AN: 53236

Other (OTH) AF: 0.0727 AC: 112 AN: 1540

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
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs10521401; hg19: chrX-94912651;