rs4656461

Variant names:

• chr1-165717968-G-A
• rs4656461

Your query was ambiguous. Multiple possible variants found:

• chr1-165717968-G-A
• chr1-165717968-G-C
• chr1-165717968-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 0.853 in 152,076 control chromosomes in the GnomAD database, including 55,544 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 0.85 (55544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 73 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.853 AC: 129576 AN: 151958 Hom.: 55507 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.853 AC: 129663 AN: 152076 Hom.: 55544 Cov.: 31 AF XY: 0.854 AC XY: 63469 AN XY: 74348

African (AFR) AF: 0.782 AC: 32431 AN: 41452

American (AMR) AF: 0.859 AC: 13116 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3262 AN: 3472

East Asian (EAS) AF: 0.990 AC: 5121 AN: 5174

South Asian (SAS) AF: 0.937 AC: 4524 AN: 4828

European-Finnish (FIN) AF: 0.818 AC: 8647 AN: 10570

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59635 AN: 67998

Other (OTH) AF: 0.865 AC: 1826 AN: 2112

Alfa AF: 0.874 Hom.: 272385

Bravo AF: 0.851

Asia WGS AF: 0.946 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4656461; hg19: chr1-165687205;