3-1674807-T-C

Variant names:

• chr3-1674807-T-C
• rs6790607

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 0.256 in 152,042 control chromosomes in the GnomAD database, including 5,762 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 0.26 (5762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38956 AN: 151926 Hom.: 5749 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.256 AC: 38997 AN: 152042 Hom.: 5762 Cov.: 32 AF XY: 0.259 AC XY: 19224 AN XY: 74324

African (AFR) AF: 0.304 AC: 12604 AN: 41488

American (AMR) AF: 0.229 AC: 3497 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3466

East Asian (EAS) AF: 0.659 AC: 3388 AN: 5144

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4826

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10574

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13785 AN: 67970

Other (OTH) AF: 0.253 AC: 533 AN: 2108

Alfa AF: 0.250 Hom.: 1974

Bravo AF: 0.258

Asia WGS AF: 0.438 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6790607; hg19: chr3-1716491;