chr3-12244234-G-T

Variant names:

• chr3-12244234-G-T
• rs1562041

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 0.654 in 152,042 control chromosomes in the GnomAD database, including 33,677 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 0.65 (33677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.654 AC: 99315 AN: 151924 Hom.: 33627 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.654 AC: 99421 AN: 152042 Hom.: 33677 Cov.: 32 AF XY: 0.660 AC XY: 49073 AN XY: 74326

African (AFR) AF: 0.794 AC: 32922 AN: 41442

American (AMR) AF: 0.638 AC: 9751 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4877 AN: 5180

South Asian (SAS) AF: 0.798 AC: 3851 AN: 4826

European-Finnish (FIN) AF: 0.625 AC: 6602 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37794 AN: 67970

Other (OTH) AF: 0.621 AC: 1310 AN: 2108

Alfa AF: 0.630 Hom.: 5390

Bravo AF: 0.657

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1562041; hg19: chr3-12285734;