12-74716021-A-C

Position:

• chr12-74716021-A-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 0.57 in 151,982 control chromosomes in the GnomAD database, including 26,377 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 0.57 (26377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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: 0.570 AC: 86503 AN: 151864 Hom.: 26326 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.570 AC: 86612 AN: 151982 Hom.: 26377 Cov.: 32 AF XY: 0.572 AC XY: 42456 AN XY: 74266

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.555

Alfa AF: 0.438 Hom.: 1932

Bravo AF: 0.591

Asia WGS AF: 0.677 AC: 2356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.81
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7967572; hg19: chr12-75109801;