12-49947924-T-C

Position:

• chr12-49947924-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 0.615 in 152,072 control chromosomes in the GnomAD database, including 30,992 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 (30992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93478 AN: 151954 Hom.: 30935 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.615 AC: 93590 AN: 152072 Hom.: 30992 Cov.: 32 AF XY: 0.616 AC XY: 45790 AN XY: 74308

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.599

Alfa AF: 0.518 Hom.: 28662

Bravo AF: 0.633

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs296736; hg19: chr12-50341707;