rs6135095

Variant names:

• chr20-1493759-C-A
• rs6135095

Your query was ambiguous. Multiple possible variants found:

• chr20-1493759-C-A
• chr20-1493759-C-G
• chr20-1493759-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.161 in 151,986 control chromosomes in the GnomAD database, including 3,188 homozygotes. 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 0.16 (3188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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: 0.161 AC: 24459 AN: 151868 Hom.: 3188 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.161 AC: 24473 AN: 151986 Hom.: 3188 Cov.: 32 AF XY: 0.168 AC XY: 12500 AN XY: 74306

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.0915

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.181

Alfa AF: 0.145 Hom.: 829

Bravo AF: 0.169

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	13
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6135095; hg19: chr20-1474405;