13-33066938-A-G

Variant names:

• chr13-33066938-A-G
• rs643780

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 0.808 in 152,278 control chromosomes in the GnomAD database, including 50,230 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 0.81 (50230 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 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: 0.808 AC: 123012 AN: 152160 Hom.: 50187 Cov.: 35

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.808 AC: 123110 AN: 152278 Hom.: 50230 Cov.: 35 AF XY: 0.808 AC XY: 60157 AN XY: 74450

African (AFR) AF: 0.723 AC: 30029 AN: 41518

American (AMR) AF: 0.811 AC: 12416 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3160 AN: 5180

South Asian (SAS) AF: 0.795 AC: 3840 AN: 4832

European-Finnish (FIN) AF: 0.884 AC: 9386 AN: 10620

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58275 AN: 68030

Other (OTH) AF: 0.835 AC: 1766 AN: 2116

Alfa AF: 0.817 Hom.: 35755

Bravo AF: 0.802

Asia WGS AF: 0.695 AC: 2420 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	1.1
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs643780; hg19: chr13-33641075;