rs10521674

Variant names:

• chrX-24334044-A-G
• rs10521674

Your query was ambiguous. Multiple possible variants found:

• chrX-24334044-A-G
• chrX-24334044-A-T

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 0.0636 in 111,082 control chromosomes in the GnomAD database, including 492 homozygotes. There are 1,927 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 0.064 (492 hom., 1927 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.0636 AC: 7060 AN: 111029 Hom.: 491 Cov.: 22 AF XY: 0.0576 AC XY: 1918 AN XY: 33279

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000562

Gnomad SAS AF: 0.0175

Gnomad FIN AF: 0.00401

Gnomad MID AF: 0.0295

Gnomad NFE AF: 0.00683

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0636 AC: 7068 AN: 111082 Hom.: 492 Cov.: 22 AF XY: 0.0578 AC XY: 1927 AN XY: 33342

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.000564

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.00401

Gnomad4 NFE AF: 0.00681

Gnomad4 OTH AF: 0.0586

Alfa AF: 0.0147 Hom.: 57

Bravo AF: 0.0729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
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: rs10521674; hg19: chrX-24352161;