chr13-104097486-G-A

Variant names:

• chr13-104097486-G-A
• rs149773673

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 0.142 in 151,806 control chromosomes in the GnomAD database, including 1,646 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 (1646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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: 0.142 AC: 21541 AN: 151686 Hom.: 1648 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.142 AC: 21541 AN: 151806 Hom.: 1646 Cov.: 31 AF XY: 0.137 AC XY: 10160 AN XY: 74166

African (AFR) AF: 0.135 AC: 5594 AN: 41392

American (AMR) AF: 0.139 AC: 2112 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3468

East Asian (EAS) AF: 0.0713 AC: 368 AN: 5160

South Asian (SAS) AF: 0.0941 AC: 452 AN: 4802

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10546

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10780 AN: 67908

Other (OTH) AF: 0.158 AC: 332 AN: 2102

Alfa AF: 0.00 Hom.: 0

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs149773673; hg19: chr13-104749836;