chr13-106902717-T-C

Variant names:

• chr13-106902717-T-C
• rs9301169

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 0.248 in 152,050 control chromosomes in the GnomAD database, including 4,973 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 0.25 (4973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.248 AC: 37626 AN: 151932 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.248 AC: 37652 AN: 152050 Hom.: 4973 Cov.: 32 AF XY: 0.245 AC XY: 18193 AN XY: 74312

African (AFR) AF: 0.173 AC: 7170 AN: 41468

American (AMR) AF: 0.185 AC: 2831 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3470

East Asian (EAS) AF: 0.188 AC: 969 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4810

European-Finnish (FIN) AF: 0.266 AC: 2803 AN: 10556

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20691 AN: 67980

Other (OTH) AF: 0.236 AC: 499 AN: 2114

Alfa AF: 0.291 Hom.: 3573

Bravo AF: 0.235

Asia WGS AF: 0.273 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9301169; hg19: chr13-107555065;