chr12-56810376-G-T

Variant names:

• chr12-56810376-G-T
• rs12367822

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 0.237 in 152,236 control chromosomes in the GnomAD database, including 4,620 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 0.24 (4620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 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: 0.238 AC: 36132 AN: 152118 Hom.: 4614 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.237 AC: 36143 AN: 152236 Hom.: 4620 Cov.: 32 AF XY: 0.233 AC XY: 17346 AN XY: 74432

African (AFR) AF: 0.161 AC: 6672 AN: 41556

American (AMR) AF: 0.247 AC: 3786 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1413 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1036 AN: 4830

European-Finnish (FIN) AF: 0.203 AC: 2153 AN: 10602

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19199 AN: 67986

Other (OTH) AF: 0.263 AC: 554 AN: 2108

Alfa AF: 0.263 Hom.: 7161

Bravo AF: 0.240

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.9
DANN	Benign	0.89
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12367822; hg19: chr12-57204160;