chrX-76228563-T-C

Variant names:

• chrX-76228563-T-C
• rs10521356

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 0.173 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

ACMG classification

Verdict is Benign. Variant got -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 AF XY: 0.158 AC XY: 5369 AN XY: 34051

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0211

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.00845

Gnomad4 FIN AF: 0.0280

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521356; hg19: chrX-75448962;