chr12-68255353-T-C

Variant names:

• chr12-68255353-T-C
• rs2227472

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 0.513 in 152,012 control chromosomes in the GnomAD database, including 20,432 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 0.51 (20432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 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: 0.513 AC: 77902 AN: 151894 Hom.: 20428 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.513 AC: 77930 AN: 152012 Hom.: 20432 Cov.: 32 AF XY: 0.510 AC XY: 37872 AN XY: 74314

African (AFR) AF: 0.424 AC: 17569 AN: 41440

American (AMR) AF: 0.514 AC: 7860 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2494 AN: 5172

South Asian (SAS) AF: 0.387 AC: 1863 AN: 4818

European-Finnish (FIN) AF: 0.536 AC: 5658 AN: 10556

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.580 AC: 39388 AN: 67954

Other (OTH) AF: 0.473 AC: 998 AN: 2112

Alfa AF: 0.451 Hom.: 1389

Bravo AF: 0.505

Asia WGS AF: 0.402 AC: 1399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2227472; hg19: chr12-68649133;