12-82000375-T-C

Variant names:

• chr12-82000375-T-C
• rs1347222

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 0.62 in 152,094 control chromosomes in the GnomAD database, including 29,308 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 0.62 (29308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94204 AN: 151976 Hom.: 29287 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.620 AC: 94262 AN: 152094 Hom.: 29308 Cov.: 33 AF XY: 0.618 AC XY: 45908 AN XY: 74344

African (AFR) AF: 0.612 AC: 25391 AN: 41476

American (AMR) AF: 0.703 AC: 10746 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2603 AN: 5170

South Asian (SAS) AF: 0.557 AC: 2693 AN: 4832

European-Finnish (FIN) AF: 0.566 AC: 5985 AN: 10572

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42295 AN: 67972

Other (OTH) AF: 0.595 AC: 1258 AN: 2114

Alfa AF: 0.624 Hom.: 29557

Bravo AF: 0.630

Asia WGS AF: 0.506 AC: 1763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1347222; hg19: chr12-82394154;