rs6686886

Variant names:

• chr1-156386688-G-A
• rs6686886

Your query was ambiguous. Multiple possible variants found:

• chr1-156386688-G-A
• chr1-156386688-G-C
• chr1-156386688-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 0.818 in 152,220 control chromosomes in the GnomAD database, including 51,287 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 0.82 (51287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 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: 0.818 AC: 124405 AN: 152102 Hom.: 51244 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.818 AC: 124511 AN: 152220 Hom.: 51287 Cov.: 32 AF XY: 0.814 AC XY: 60553 AN XY: 74410

African (AFR) AF: 0.821 AC: 34078 AN: 41520

American (AMR) AF: 0.778 AC: 11902 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3053 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2780 AN: 5166

South Asian (SAS) AF: 0.804 AC: 3879 AN: 4822

European-Finnish (FIN) AF: 0.786 AC: 8335 AN: 10608

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57682 AN: 68020

Other (OTH) AF: 0.823 AC: 1739 AN: 2114

Alfa AF: 0.839 Hom.: 216635

Bravo AF: 0.816

Asia WGS AF: 0.731 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6686886; hg19: chr1-156356480;