3-139804291-C-A

Variant names:

• chr3-139804291-C-A
• rs952797

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 0.407 in 152,062 control chromosomes in the GnomAD database, including 12,761 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 0.41 (12761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 6 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 (AMR) allele frequency at 95% confidence interval = 0.509 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: 0.407 AC: 61811 AN: 151944 Hom.: 12751 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.407 AC: 61865 AN: 152062 Hom.: 12761 Cov.: 32 AF XY: 0.408 AC XY: 30333 AN XY: 74330

African (AFR) AF: 0.410 AC: 17021 AN: 41486

American (AMR) AF: 0.518 AC: 7920 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1438 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1712 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4258 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27101 AN: 67948

Other (OTH) AF: 0.398 AC: 839 AN: 2110

Alfa AF: 0.424 Hom.: 2578

Bravo AF: 0.415

Asia WGS AF: 0.326 AC: 1131 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	6.2
DANN	Benign	0.58
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs952797; hg19: chr3-139523133;