rs6637820

Variant names:

• chrX-131266334-C-A
• rs6637820

Your query was ambiguous. Multiple possible variants found:

• chrX-131266334-C-A
• chrX-131266334-C-G
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;