13-30129807-C-A

Variant names:

• chr13-30129807-C-A
• rs1409506

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 0.139 in 152,100 control chromosomes in the GnomAD database, including 1,745 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 0.14 (1745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21061 AN: 151982 Hom.: 1748 Cov.: 32

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.139 AC: 21071 AN: 152100 Hom.: 1745 Cov.: 32 AF XY: 0.145 AC XY: 10752 AN XY: 74348

African (AFR) AF: 0.0714 AC: 2966 AN: 41512

American (AMR) AF: 0.144 AC: 2204 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5162

South Asian (SAS) AF: 0.265 AC: 1274 AN: 4810

European-Finnish (FIN) AF: 0.198 AC: 2093 AN: 10570

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10353 AN: 67984

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.145 Hom.: 6937

Bravo AF: 0.128

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1409506; hg19: chr13-30703944;