12-13983207-T-C

Variant names:

• chr12-13983207-T-C
• rs12368476

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 0.429 in 152,178 control chromosomes in the GnomAD database, including 16,820 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 0.43 (16820 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.59 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: 0.429 AC: 65292 AN: 152060 Hom.: 16821 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.429 AC: 65294 AN: 152178 Hom.: 16820 Cov.: 33 AF XY: 0.431 AC XY: 32096 AN XY: 74386

African (AFR) AF: 0.127 AC: 5295 AN: 41534

American (AMR) AF: 0.600 AC: 9181 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3091 AN: 5162

South Asian (SAS) AF: 0.574 AC: 2766 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4842 AN: 10590

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36879 AN: 67984

Other (OTH) AF: 0.458 AC: 970 AN: 2116

Alfa AF: 0.503 Hom.: 58800

Bravo AF: 0.428

Asia WGS AF: 0.555 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs12368476; hg19: chr12-14136141;