12-91075973-C-T

Position:

• chr12-91075973-C-T

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 0.764 in 152,030 control chromosomes in the GnomAD database, including 45,748 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 0.76 (45748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.91 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: 0.764 AC: 116074 AN: 151912 Hom.: 45735 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.764 AC: 116123 AN: 152030 Hom.: 45748 Cov.: 33 AF XY: 0.772 AC XY: 57380 AN XY: 74326

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.779

Alfa AF: 0.825 Hom.: 75079

Bravo AF: 0.746

Asia WGS AF: 0.898 AC: 3106 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777287; hg19: chr12-91469750;