chr13-85038134-G-C

Variant names:

• chr13-85038134-G-C
• rs9319109

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 0.371 in 151,856 control chromosomes in the GnomAD database, including 11,503 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 0.37 (11503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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: 0.371 AC: 56311 AN: 151738 Hom.: 11483 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.371 AC: 56371 AN: 151856 Hom.: 11503 Cov.: 32 AF XY: 0.365 AC XY: 27075 AN XY: 74212

African (AFR) AF: 0.541 AC: 22430 AN: 41452

American (AMR) AF: 0.260 AC: 3966 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3468

East Asian (EAS) AF: 0.113 AC: 585 AN: 5174

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2928 AN: 10514

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22563 AN: 67862

Other (OTH) AF: 0.349 AC: 738 AN: 2112

Alfa AF: 0.362 Hom.: 1302

Bravo AF: 0.373

Asia WGS AF: 0.242 AC: 837 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs9319109; hg19: chr13-85612269;