chr13-29910725-G-A

Variant names:

• chr13-29910725-G-A
• rs1547162

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 0.331 in 152,034 control chromosomes in the GnomAD database, including 8,598 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 0.33 (8598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50186 AN: 151916 Hom.: 8571 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.331 AC: 50266 AN: 152034 Hom.: 8598 Cov.: 32 AF XY: 0.332 AC XY: 24685 AN XY: 74318

African (AFR) AF: 0.417 AC: 17276 AN: 41448

American (AMR) AF: 0.253 AC: 3869 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2155 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1421 AN: 4828

European-Finnish (FIN) AF: 0.312 AC: 3297 AN: 10568

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20083 AN: 67960

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.302 Hom.: 15601

Bravo AF: 0.330

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.31
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs1547162; hg19: chr13-30484862;