12-33149504-G-T

Variant names:

• chr12-33149504-G-T
• rs10772040

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 0.143 in 143,528 control chromosomes in the GnomAD database, including 4,814 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 0.14 (4814 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 20560 AN: 143414 Hom.: 4810 Cov.: 28

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0210

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.143 AC: 20580 AN: 143528 Hom.: 4814 Cov.: 28 AF XY: 0.151 AC XY: 10543 AN XY: 69874

African (AFR) AF: 0.145 AC: 5862 AN: 40536

American (AMR) AF: 0.152 AC: 2101 AN: 13814

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 597 AN: 3216

East Asian (EAS) AF: 0.828 AC: 4058 AN: 4900

South Asian (SAS) AF: 0.320 AC: 1431 AN: 4468

European-Finnish (FIN) AF: 0.0810 AC: 803 AN: 9912

Middle Eastern (MID) AF: 0.104 AC: 28 AN: 270

European-Non Finnish (NFE) AF: 0.0849 AC: 5398 AN: 63612

Other (OTH) AF: 0.146 AC: 284 AN: 1944

Alfa AF: 0.103 Hom.: 1461

Asia WGS AF: 0.520 AC: 1737 AN: 3346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.46
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10772040; hg19: chr12-33302438;