12-82000375-T-C

Variant names:

• chr12-82000375-T-C
• rs1347222

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.620 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

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.595

Alfa AF: 0.621 Hom.: 21233

Bravo AF: 0.630

Asia WGS AF: 0.506 AC: 1763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347222; hg19: chr12-82394154;