rs6135095

Variant names:

• chr20-1493759-C-A
• rs6135095
• ENST00000824325.1:n.238+1959C>A

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. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000824325.1(ENSG00000307156):​n.238+1959C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000307156 ENST00000824325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 12 publications found

Genes affected

ENSG00000307156 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000307156	ENST00000824325.1	n.238+1959C>A		intron_variant	Intron 1 of 1
ENSG00000307156	ENST00000824326.1	n.92+1208C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.108 AC: 4487 AN: 41448

American (AMR) AF: 0.228 AC: 3475 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 598 AN: 3466

East Asian (EAS) AF: 0.738 AC: 3794 AN: 5144

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4804

European-Finnish (FIN) AF: 0.0915 AC: 967 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9143 AN: 67966

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.144 Hom.: 914

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6135095; hg19: chr20-1474405;