chr12-91005279-C-T

Position:

• chr12-91005279-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 0.88 in 152,024 control chromosomes in the GnomAD database, including 58,864 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 0.88 (58864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.924 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: 0.880 AC: 133649 AN: 151906 Hom.: 58825 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.880 AC: 133739 AN: 152024 Hom.: 58864 Cov.: 32 AF XY: 0.884 AC XY: 65628 AN XY: 74254

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.872

Alfa AF: 0.883 Hom.: 8188

Bravo AF: 0.875

Asia WGS AF: 0.936 AC: 3248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920748; hg19: chr12-91399056;