chr3-80412274-C-A

Variant names:

• chr3-80412274-C-A
• rs6809002

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 0.385 in 152,020 control chromosomes in the GnomAD database, including 11,778 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 0.38 (11778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.55 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: 0.385 AC: 58440 AN: 151902 Hom.: 11769 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.385 AC: 58478 AN: 152020 Hom.: 11778 Cov.: 32 AF XY: 0.392 AC XY: 29164 AN XY: 74308

African (AFR) AF: 0.266 AC: 11048 AN: 41482

American (AMR) AF: 0.448 AC: 6834 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2733 AN: 4818

European-Finnish (FIN) AF: 0.408 AC: 4316 AN: 10570

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.414 AC: 28129 AN: 67952

Other (OTH) AF: 0.375 AC: 793 AN: 2114

Alfa AF: 0.394 Hom.: 15027

Bravo AF: 0.377

Asia WGS AF: 0.517 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.73
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs6809002; hg19: chr3-80461424;