rs10521356

Variant names:

• chrX-76228563-T-C
• rs10521356

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 0.173 in 111,899 control chromosomes in the GnomAD database, including 3,591 homozygotes. There are 5,408 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 0.17 (3591 hom., 5408 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.173 AC: 19313 AN: 111845 Hom.: 3585 Cov.: 23

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.0247

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.00988

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0717

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.173 AC: 19362 AN: 111899 Hom.: 3591 Cov.: 23 AF XY: 0.159 AC XY: 5408 AN XY: 34115

African (AFR) AF: 0.560 AC: 17082 AN: 30525

American (AMR) AF: 0.101 AC: 1062 AN: 10565

Ashkenazi Jewish (ASJ) AF: 0.0211 AC: 56 AN: 2651

East Asian (EAS) AF: 0.0407 AC: 145 AN: 3561

South Asian (SAS) AF: 0.00845 AC: 23 AN: 2722

European-Finnish (FIN) AF: 0.0280 AC: 173 AN: 6182

Middle Eastern (MID) AF: 0.0783 AC: 17 AN: 217

European-Non Finnish (NFE) AF: 0.0108 AC: 576 AN: 53257

Other (OTH) AF: 0.138 AC: 211 AN: 1532

Alfa AF: 0.107 Hom.: 724

Bravo AF: 0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.52
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs10521356; hg19: chrX-75448962;