rs4279078

Variant names:

• chr3-12273347-G-A
• rs4279078

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 0.103 in 152,152 control chromosomes in the GnomAD database, including 1,055 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 0.10 (1055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.103 AC: 15652 AN: 152034 Hom.: 1057 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.103 AC: 15643 AN: 152152 Hom.: 1055 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74392

African (AFR) AF: 0.0520 AC: 2157 AN: 41510

American (AMR) AF: 0.124 AC: 1894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1918 AN: 5174

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4824

European-Finnish (FIN) AF: 0.0623 AC: 658 AN: 10570

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8074 AN: 67998

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.113 Hom.: 3375

Bravo AF: 0.107

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs4279078; hg19: chr3-12314846; COSMIC: COSV68623614;