chr3-3670552-C-T

Variant names:

• chr3-3670552-C-T
• rs764593

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 0.0946 in 152,162 control chromosomes in the GnomAD database, including 978 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 0.095 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.0946 AC: 14377 AN: 152044 Hom.: 972 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0946 AC: 14391 AN: 152162 Hom.: 978 Cov.: 32 AF XY: 0.0973 AC XY: 7241 AN XY: 74390

African (AFR) AF: 0.0220 AC: 915 AN: 41546

American (AMR) AF: 0.194 AC: 2957 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3468

East Asian (EAS) AF: 0.188 AC: 968 AN: 5162

South Asian (SAS) AF: 0.0712 AC: 343 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1451 AN: 10580

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7017 AN: 67986

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0997 Hom.: 2801

Bravo AF: 0.0961

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs764593; hg19: chr3-3712236;