12-91080645-C-T

Variant names:

• chr12-91080645-C-T
• rs991427

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 0.166 in 151,770 control chromosomes in the GnomAD database, including 2,546 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 0.17 (2546 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25238 AN: 151652 Hom.: 2541 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.166 AC: 25265 AN: 151770 Hom.: 2546 Cov.: 31 AF XY: 0.160 AC XY: 11882 AN XY: 74152

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.0562

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.163

Alfa AF: 0.0949 Hom.: 179

Bravo AF: 0.177

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991427; hg19: chr12-91474422;