chr3-12244234-G-T

Variant names:

• chr3-12244234-G-T
• rs1562041

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 0.654 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.621

Alfa AF: 0.626 Hom.: 5146

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562041; hg19: chr3-12285734;