chr13-33075809-G-T

Variant names:

• chr13-33075809-G-T
• rs534184

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 0.379 in 152,062 control chromosomes in the GnomAD database, including 12,364 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 0.38 (12364 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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: 0.379 AC: 57580 AN: 151944 Hom.: 12345 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.379 AC: 57621 AN: 152062 Hom.: 12364 Cov.: 33 AF XY: 0.382 AC XY: 28421 AN XY: 74322

African (AFR) AF: 0.190 AC: 7861 AN: 41470

American (AMR) AF: 0.553 AC: 8444 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5174

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4814

European-Finnish (FIN) AF: 0.479 AC: 5060 AN: 10560

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30261 AN: 67980

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.277 Hom.: 761

Bravo AF: 0.381

Asia WGS AF: 0.343 AC: 1198 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	0.80
DANN	Benign	0.58
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs534184; hg19: chr13-33649946;