chr13-33723918-C-T

Position:

• chr13-33723918-C-T

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 0.0771 in 152,128 control chromosomes in the GnomAD database, including 992 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 0.077 (992 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33723918C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11697 AN: 152010 Hom.: 988 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0771 AC: 11735 AN: 152128 Hom.: 992 Cov.: 33 AF XY: 0.0784 AC XY: 5831 AN XY: 74364

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0728

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.00538 Hom.: 2

Bravo AF: 0.0880

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7318085; hg19: chr13-34298055;