13-33067646-T-G

Variant names:

• chr13-33067646-T-G
• rs17643689

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0557 Hom.: 73

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17643689; hg19: chr13-33641783;