13-30773137-C-T

Position:

• chr13-30773137-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 0.188 in 152,232 control chromosomes in the GnomAD database, including 3,715 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 0.19 (3715 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30773137C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28519 AN: 152114 Hom.: 3703 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.188 AC: 28562 AN: 152232 Hom.: 3715 Cov.: 33 AF XY: 0.181 AC XY: 13473 AN XY: 74430

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.171

Alfa AF: 0.0972 Hom.: 256

Bravo AF: 0.204

Asia WGS AF: 0.154 AC: 535 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	1.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4769063; hg19: chr13-31347274;