12-91075283-G-C

Position:

• chr12-91075283-G-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 0.561 in 151,826 control chromosomes in the GnomAD database, including 25,777 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 0.56 (25777 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91075283G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85079 AN: 151708 Hom.: 25771 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.561 AC: 85120 AN: 151826 Hom.: 25777 Cov.: 30 AF XY: 0.565 AC XY: 41889 AN XY: 74198

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.573

Alfa AF: 0.598 Hom.: 3543

Bravo AF: 0.536

Asia WGS AF: 0.599 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10745551; hg19: chr12-91469060;