13-33067646-T-G

Variant names:

• chr13-33067646-T-G
• rs17643689

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 152,248 control chromosomes in the GnomAD database, including 1,820 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 0.14 (1820 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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: 0.143 AC: 21785 AN: 152132 Hom.: 1819 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.143 AC: 21796 AN: 152248 Hom.: 1820 Cov.: 33 AF XY: 0.146 AC XY: 10849 AN XY: 74442

African (AFR) AF: 0.108 AC: 4487 AN: 41542

American (AMR) AF: 0.170 AC: 2600 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2012 AN: 5170

South Asian (SAS) AF: 0.205 AC: 987 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9748 AN: 68014

Other (OTH) AF: 0.134 AC: 283 AN: 2116

Alfa AF: 0.0576 Hom.: 77

Bravo AF: 0.142

Asia WGS AF: 0.296 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.095
DANN	Benign	0.77
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17643689; hg19: chr13-33641783;