12-91770525-C-T

Variant names:

• chr12-91770525-C-T
• rs10777332

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 0.203 in 151,966 control chromosomes in the GnomAD database, including 3,392 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 0.20 (3392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

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 = 0.289 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: 0.203 AC: 30798 AN: 151848 Hom.: 3389 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0846

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.203 AC: 30810 AN: 151966 Hom.: 3392 Cov.: 32 AF XY: 0.198 AC XY: 14669 AN XY: 74252

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0844

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.208

Alfa AF: 0.169 Hom.: 3660

Bravo AF: 0.213

Asia WGS AF: 0.122 AC: 425 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	5.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777332; hg19: chr12-92164302;