chr12-87246742-T-C

Position:

• chr12-87246742-T-C

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 0.448 in 152,024 control chromosomes in the GnomAD database, including 16,326 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 0.45 (16326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68009 AN: 151904 Hom.: 16303 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.448 AC: 68077 AN: 152024 Hom.: 16326 Cov.: 32 AF XY: 0.452 AC XY: 33566 AN XY: 74310

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.476

Alfa AF: 0.502 Hom.: 39444

Bravo AF: 0.452

Asia WGS AF: 0.538 AC: 1868 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11104365; hg19: chr12-87640519;