13-30773137-C-T

Variant names:

• chr13-30773137-C-T
• rs4769063

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 0.188 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.367 AC: 15213 AN: 41488

American (AMR) AF: 0.146 AC: 2240 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3472

East Asian (EAS) AF: 0.103 AC: 535 AN: 5186

South Asian (SAS) AF: 0.150 AC: 726 AN: 4828

European-Finnish (FIN) AF: 0.0590 AC: 626 AN: 10616

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8115 AN: 68018

Other (OTH) AF: 0.171 AC: 361 AN: 2116

Alfa AF: 0.109 Hom.: 314

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs4769063; hg19: chr13-31347274;