chr13-103550825-G-A

Variant names:

• chr13-103550825-G-A
• rs9300826

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 0.0858 in 152,020 control chromosomes in the GnomAD database, including 895 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 0.086 (895 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0859 AC: 13045 AN: 151902 Hom.: 895 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0858 AC: 13045 AN: 152020 Hom.: 895 Cov.: 33 AF XY: 0.0899 AC XY: 6679 AN XY: 74266

African (AFR) AF: 0.0214 AC: 890 AN: 41508

American (AMR) AF: 0.0518 AC: 791 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3472

East Asian (EAS) AF: 0.107 AC: 551 AN: 5166

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2754 AN: 10518

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7498 AN: 67960

Other (OTH) AF: 0.0692 AC: 146 AN: 2110

Alfa AF: 0.0962 Hom.: 433

Bravo AF: 0.0687

Asia WGS AF: 0.0800 AC: 276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.18
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs9300826; hg19: chr13-104203175;