12-17965996-C-T

Variant names:

• chr12-17965996-C-T
• rs7971307

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 0.554 in 151,824 control chromosomes in the GnomAD database, including 24,022 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 0.55 (24022 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.554 AC: 84103 AN: 151706 Hom.: 24018 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.554 AC: 84131 AN: 151824 Hom.: 24022 Cov.: 31 AF XY: 0.564 AC XY: 41898 AN XY: 74228

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.544

Alfa AF: 0.572 Hom.: 25223

Bravo AF: 0.530

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7971307; hg19: chr12-18118930;