13-33817815-T-G

Variant names:

• chr13-33817815-T-G
• rs2147668

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 0.229 in 152,118 control chromosomes in the GnomAD database, including 6,334 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 0.23 (6334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 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: 0.229 AC: 34749 AN: 152000 Hom.: 6305 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.229 AC: 34835 AN: 152118 Hom.: 6334 Cov.: 32 AF XY: 0.230 AC XY: 17121 AN XY: 74382

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.230

Alfa AF: 0.118 Hom.: 2761

Bravo AF: 0.262

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2147668; hg19: chr13-34391952;