12-17965996-C-T

Variant names:

• chr12-17965996-C-T
• rs7971307

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.436 AC: 18033 AN: 41354

American (AMR) AF: 0.505 AC: 7701 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3944 AN: 5150

South Asian (SAS) AF: 0.710 AC: 3413 AN: 4808

European-Finnish (FIN) AF: 0.735 AC: 7773 AN: 10578

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39682 AN: 67916

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.569 Hom.: 35714

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7971307; hg19: chr12-18118930;