rs10521734

Variant names:

• chrX-125660469-A-G
• rs10521734

Your query was ambiguous. Multiple possible variants found:

• chrX-125660469-A-G
• chrX-125660469-A-T

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 0.308 in 109,984 control chromosomes in the GnomAD database, including 3,948 homozygotes. There are 9,603 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 0.31 (3948 hom., 9603 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 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: 0.308 AC: 33903 AN: 109934 Hom.: 3949 Cov.: 22

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.308 AC: 33924 AN: 109984 Hom.: 3948 Cov.: 22 AF XY: 0.298 AC XY: 9603 AN XY: 32278

African (AFR) AF: 0.237 AC: 7193 AN: 30325

American (AMR) AF: 0.363 AC: 3722 AN: 10263

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1146 AN: 2620

East Asian (EAS) AF: 0.148 AC: 516 AN: 3476

South Asian (SAS) AF: 0.258 AC: 666 AN: 2579

European-Finnish (FIN) AF: 0.307 AC: 1758 AN: 5727

Middle Eastern (MID) AF: 0.351 AC: 73 AN: 208

European-Non Finnish (NFE) AF: 0.344 AC: 18094 AN: 52636

Other (OTH) AF: 0.320 AC: 474 AN: 1482

Alfa AF: 0.315 Hom.: 2356

Bravo AF: 0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.54
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs10521734; hg19: chrX-124794465;