12-91079228-T-C

Position:

• chr12-91079228-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 0.587 in 151,348 control chromosomes in the GnomAD database, including 28,639 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 0.59 (28639 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) 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: 0.587 AC: 88737 AN: 151230 Hom.: 28629 Cov.: 30

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.587 AC: 88767 AN: 151348 Hom.: 28639 Cov.: 30 AF XY: 0.594 AC XY: 43916 AN XY: 73922

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.611

Alfa AF: 0.682 Hom.: 16253

Bravo AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859105; hg19: chr12-91473005;