rs12639469

Positions:

• chr3-161800073-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.161800073G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;