rs294278

Variant names:

• chr3-31086419-T-C
• rs294278

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 0.425 in 152,042 control chromosomes in the GnomAD database, including 15,494 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 0.43 (15494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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: 0.425 AC: 64594 AN: 151924 Hom.: 15482 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.425 AC: 64634 AN: 152042 Hom.: 15494 Cov.: 32 AF XY: 0.422 AC XY: 31378 AN XY: 74350

African (AFR) AF: 0.214 AC: 8881 AN: 41500

American (AMR) AF: 0.317 AC: 4848 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1953 AN: 5162

South Asian (SAS) AF: 0.357 AC: 1722 AN: 4826

European-Finnish (FIN) AF: 0.559 AC: 5914 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38098 AN: 67930

Other (OTH) AF: 0.458 AC: 966 AN: 2110

Alfa AF: 0.497 Hom.: 11521

Bravo AF: 0.397

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.1
DANN	Benign	0.89
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs294278; hg19: chr3-31127911;