12-33371147-C-T

Variant names:

• chr12-33371147-C-T
• rs1905414

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.471 in 151,936 control chromosomes in the GnomAD database, including 19,701 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 0.47 (19701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.470 AC: 71389 AN: 151820 Hom.: 19649 Cov.: 33

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.471 AC: 71496 AN: 151936 Hom.: 19701 Cov.: 33 AF XY: 0.475 AC XY: 35270 AN XY: 74242

African (AFR) AF: 0.753 AC: 31235 AN: 41502

American (AMR) AF: 0.485 AC: 7389 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1249 AN: 3464

East Asian (EAS) AF: 0.611 AC: 3156 AN: 5164

South Asian (SAS) AF: 0.474 AC: 2282 AN: 4814

European-Finnish (FIN) AF: 0.362 AC: 3807 AN: 10526

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20990 AN: 67900

Other (OTH) AF: 0.447 AC: 945 AN: 2112

Alfa AF: 0.356 Hom.: 5579

Bravo AF: 0.492

Asia WGS AF: 0.563 AC: 1952 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	18
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1905414; hg19: chr12-33524082;