chr12-91069931-A-G

Position:

• chr12-91069931-A-G

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 0.167 in 152,040 control chromosomes in the GnomAD database, including 2,639 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 0.17 (2639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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 (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25305 AN: 151922 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.167 AC: 25341 AN: 152040 Hom.: 2639 Cov.: 32 AF XY: 0.167 AC XY: 12399 AN XY: 74322

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.143

Alfa AF: 0.136 Hom.: 779

Bravo AF: 0.180

Asia WGS AF: 0.193 AC: 665 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12231819; hg19: chr12-91463708;