chr12-33064859-T-G

Variant names:

• chr12-33064859-T-G
• rs12424662

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 0.575 in 151,928 control chromosomes in the GnomAD database, including 26,368 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 0.57 (26368 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.575 AC: 87216 AN: 151810 Hom.: 26324 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.575 AC: 87321 AN: 151928 Hom.: 26368 Cov.: 33 AF XY: 0.577 AC XY: 42847 AN XY: 74282

African (AFR) AF: 0.733 AC: 30406 AN: 41458

American (AMR) AF: 0.508 AC: 7765 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4523 AN: 5178

South Asian (SAS) AF: 0.603 AC: 2904 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4954 AN: 10512

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33367 AN: 67914

Other (OTH) AF: 0.568 AC: 1196 AN: 2106

Alfa AF: 0.512 Hom.: 9623

Bravo AF: 0.585

Asia WGS AF: 0.748 AC: 2584 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	1.3
DANN	Benign	0.94
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12424662; hg19: chr12-33217793;