3-161800073-G-A

Variant names:

• chr3-161800073-G-A
• rs12639469

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 0.436 in 151,666 control chromosomes in the GnomAD database, including 15,192 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 0.44 (15192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.436 AC: 66144 AN: 151548 Hom.: 15171 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.436 AC: 66202 AN: 151666 Hom.: 15192 Cov.: 32 AF XY: 0.442 AC XY: 32778 AN XY: 74128

African (AFR) AF: 0.340 AC: 14071 AN: 41338

American (AMR) AF: 0.493 AC: 7515 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3462

East Asian (EAS) AF: 0.851 AC: 4373 AN: 5136

South Asian (SAS) AF: 0.415 AC: 2001 AN: 4820

European-Finnish (FIN) AF: 0.521 AC: 5466 AN: 10494

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29976 AN: 67862

Other (OTH) AF: 0.433 AC: 912 AN: 2106

Alfa AF: 0.438 Hom.: 20025

Bravo AF: 0.438

Asia WGS AF: 0.643 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.23
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs12639469; hg19: chr3-161517861;