rs12639469

Variant names:

• chr3-161800073-G-A
• rs12639469

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.433

Alfa AF: 0.439 Hom.: 15866

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12639469; hg19: chr3-161517861;