rs4680612

Variant names:

• chr3-165891643-G-A
• rs4680612

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 0.946 in 152,280 control chromosomes in the GnomAD database, including 68,140 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 0.95 (68140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143881 AN: 152162 Hom.: 68091 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.946 AC: 143991 AN: 152280 Hom.: 68140 Cov.: 32 AF XY: 0.947 AC XY: 70472 AN XY: 74452

African (AFR) AF: 0.905 AC: 37570 AN: 41536

American (AMR) AF: 0.961 AC: 14694 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3366 AN: 3470

East Asian (EAS) AF: 0.915 AC: 4733 AN: 5170

South Asian (SAS) AF: 0.919 AC: 4438 AN: 4830

European-Finnish (FIN) AF: 0.985 AC: 10465 AN: 10622

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65553 AN: 68040

Other (OTH) AF: 0.947 AC: 2002 AN: 2114

Alfa AF: 0.960 Hom.: 30502

Bravo AF: 0.941

Asia WGS AF: 0.933 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.088
DANN	Benign	0.51
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4680612; hg19: chr3-165609431;