rs2817461

Variant names:

• chr6-156591878-G-A
• rs2817461

Your query was ambiguous. Multiple possible variants found:

• chr6-156591878-G-A
• chr6-156591878-G-C
• chr6-156591878-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.282 in 151,998 control chromosomes in the GnomAD database, including 6,513 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 0.28 (6513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.282 AC: 42756 AN: 151880 Hom.: 6505 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.282 AC: 42794 AN: 151998 Hom.: 6513 Cov.: 32 AF XY: 0.280 AC XY: 20833 AN XY: 74272

African (AFR) AF: 0.174 AC: 7211 AN: 41466

American (AMR) AF: 0.287 AC: 4391 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3472

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5176

South Asian (SAS) AF: 0.256 AC: 1230 AN: 4810

European-Finnish (FIN) AF: 0.354 AC: 3729 AN: 10538

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23224 AN: 67948

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.312 Hom.: 25064

Bravo AF: 0.269

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.77
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2817461; hg19: chr6-156913012;