rs10521940

Variant names:

• chrX-27973414-G-A
• rs10521940

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 0.184 in 111,112 control chromosomes in the GnomAD database, including 2,495 homozygotes. There are 5,818 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 0.18 (2495 hom., 5818 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.184 AC: 20417 AN: 111065 Hom.: 2497 Cov.: 23

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.00876

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.184 AC: 20454 AN: 111112 Hom.: 2495 Cov.: 23 AF XY: 0.174 AC XY: 5818 AN XY: 33386

African (AFR) AF: 0.447 AC: 13588 AN: 30391

American (AMR) AF: 0.0991 AC: 1039 AN: 10489

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 170 AN: 2645

East Asian (EAS) AF: 0.0702 AC: 247 AN: 3519

South Asian (SAS) AF: 0.103 AC: 276 AN: 2674

European-Finnish (FIN) AF: 0.111 AC: 666 AN: 5985

Middle Eastern (MID) AF: 0.112 AC: 24 AN: 215

European-Non Finnish (NFE) AF: 0.0794 AC: 4205 AN: 52991

Other (OTH) AF: 0.153 AC: 233 AN: 1518

Alfa AF: 0.108 Hom.: 4443

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.53
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs10521940; hg19: chrX-27991531;