12-17291799-A-T

Variant names:

• chr12-17291799-A-T
• rs2965667

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 0.959 in 152,278 control chromosomes in the GnomAD database, including 70,016 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 0.96 (70016 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.964 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: 0.959 AC: 145911 AN: 152160 Hom.: 69966 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.959 AC: 146017 AN: 152278 Hom.: 70016 Cov.: 33 AF XY: 0.958 AC XY: 71345 AN XY: 74450

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.959

Alfa AF: 0.968 Hom.: 3862

Bravo AF: 0.959

Asia WGS AF: 0.913 AC: 3169 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2965667; hg19: chr12-17444733;