3-165865082-C-T

Variant names:

• chr3-165865082-C-T
• rs7645596

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 0.667 in 152,008 control chromosomes in the GnomAD database, including 34,798 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 0.67 (34798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.667 AC: 101291 AN: 151890 Hom.: 34771 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.667 AC: 101362 AN: 152008 Hom.: 34798 Cov.: 32 AF XY: 0.671 AC XY: 49824 AN XY: 74298

African (AFR) AF: 0.483 AC: 20004 AN: 41420

American (AMR) AF: 0.763 AC: 11654 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3472

East Asian (EAS) AF: 0.800 AC: 4128 AN: 5162

South Asian (SAS) AF: 0.723 AC: 3486 AN: 4820

European-Finnish (FIN) AF: 0.764 AC: 8066 AN: 10558

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49315 AN: 67988

Other (OTH) AF: 0.678 AC: 1429 AN: 2108

Alfa AF: 0.705 Hom.: 24938

Bravo AF: 0.657

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.029
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7645596; hg19: chr3-165582870;