chr13-33723187-T-C

Position:

• chr13-33723187-T-C

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 0.0773 in 152,226 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: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11729 AN: 152108 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0773 AC: 11767 AN: 152226 Hom.: 992 Cov.: 32 AF XY: 0.0786 AC XY: 5854 AN XY: 74444

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0132 Hom.: 12

Bravo AF: 0.0881

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	-0.86
CADD	Benign	12
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9598026; hg19: chr13-34297324;