12-115137888-A-T

Variant names:

• chr12-115137888-A-T
• rs3858646

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 0.141 in 152,228 control chromosomes in the GnomAD database, including 1,607 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 0.14 (1607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 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: 0.141 AC: 21406 AN: 152110 Hom.: 1608 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.141 AC: 21418 AN: 152228 Hom.: 1607 Cov.: 33 AF XY: 0.144 AC XY: 10727 AN XY: 74440

African (AFR) AF: 0.114 AC: 4716 AN: 41522

American (AMR) AF: 0.108 AC: 1658 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.142 AC: 736 AN: 5174

South Asian (SAS) AF: 0.0828 AC: 400 AN: 4832

European-Finnish (FIN) AF: 0.247 AC: 2618 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10197 AN: 68022

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.0696 Hom.: 94

Bravo AF: 0.129

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.38
DANN	Benign	0.51
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs3858646; hg19: chr12-115575693;