rs12485321

Variant names:

• chr3-108303-G-A
• rs12485321

Your query was ambiguous. Multiple possible variants found:

• chr3-108303-G-A
• chr3-108303-G-C

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 0.371 in 151,730 control chromosomes in the GnomAD database, including 10,937 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 0.37 (10937 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.371 AC: 56255 AN: 151608 Hom.: 10929 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.371 AC: 56301 AN: 151730 Hom.: 10937 Cov.: 33 AF XY: 0.369 AC XY: 27333 AN XY: 74144

African (AFR) AF: 0.323 AC: 13340 AN: 41252

American (AMR) AF: 0.341 AC: 5201 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1683 AN: 3466

East Asian (EAS) AF: 0.0678 AC: 351 AN: 5174

South Asian (SAS) AF: 0.379 AC: 1825 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3779 AN: 10530

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28774 AN: 67936

Other (OTH) AF: 0.397 AC: 838 AN: 2112

Alfa AF: 0.400 Hom.: 35801

Bravo AF: 0.365

Asia WGS AF: 0.260 AC: 904 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	0.030
DANN	Benign	0.65
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs12485321; hg19: chr3-149986;