rs10521940

Positions:

• chrX-27973414-G-A

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 0.184 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.184 AC: 20417 AN: 111065 Hom.: 2497 Cov.: 23 AF XY: 0.174 AC XY: 5786 AN XY: 33329

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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.0702

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.153

Alfa AF: 0.104 Hom.: 3568

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521940; hg19: chrX-27991531;