12-12268125-A-T

Variant names:

• chr12-12268125-A-T
• rs12309338

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 0.0717 in 152,252 control chromosomes in the GnomAD database, including 467 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 0.072 (467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0928 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: 0.0717 AC: 10902 AN: 152134 Hom.: 466 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0717 AC: 10909 AN: 152252 Hom.: 467 Cov.: 32 AF XY: 0.0709 AC XY: 5282 AN XY: 74448

African (AFR) AF: 0.0354 AC: 1473 AN: 41560

American (AMR) AF: 0.0969 AC: 1482 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0829 AC: 287 AN: 3464

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4828

European-Finnish (FIN) AF: 0.0874 AC: 927 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6260 AN: 67990

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0313 Hom.: 23

Bravo AF: 0.0737

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs12309338; hg19: chr12-12421059;