12-118617212-A-T

Variant names:

• chr12-118617212-A-T
• rs2730550

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 0.309 in 152,048 control chromosomes in the GnomAD database, including 7,970 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 0.31 (7970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.309 AC: 46896 AN: 151930 Hom.: 7960 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.309 AC: 46933 AN: 152048 Hom.: 7970 Cov.: 32 AF XY: 0.313 AC XY: 23243 AN XY: 74314

African (AFR) AF: 0.405 AC: 16797 AN: 41446

American (AMR) AF: 0.382 AC: 5842 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3144 AN: 5152

South Asian (SAS) AF: 0.322 AC: 1547 AN: 4804

European-Finnish (FIN) AF: 0.213 AC: 2252 AN: 10590

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15300 AN: 67990

Other (OTH) AF: 0.329 AC: 693 AN: 2106

Alfa AF: 0.265 Hom.: 662

Bravo AF: 0.328

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs2730550; hg19: chr12-119055017;