rs6637820

chrX-131266334-C-AchrX-131266334-C-GchrX-131266334-C-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 0.136 in 109,951 control chromosomes in the GnomAD database, including 1,254 homozygotes. There are 4,524 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 0.14 (1254 hom., 4524 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 14951 AN: 109897 Hom.: 1256 Cov.: 22 AF XY: 0.140 AC XY: 4518 AN XY: 32229

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0616

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0739

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 14952 AN: 109951 Hom.: 1254 Cov.: 22 AF XY: 0.140 AC XY: 4524 AN XY: 32293

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0739

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0953 Hom.: 7090

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.011
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6637820; hg19: chrX-130400308;