rs9319110

Variant names:

• chr13-85038253-C-T
• rs9319110

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 0.334 in 151,864 control chromosomes in the GnomAD database, including 8,834 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 (8834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50678 AN: 151746 Hom.: 8822 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.334 AC: 50726 AN: 151864 Hom.: 8834 Cov.: 32 AF XY: 0.329 AC XY: 24405 AN XY: 74214

African (AFR) AF: 0.413 AC: 17098 AN: 41436

American (AMR) AF: 0.246 AC: 3757 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3468

East Asian (EAS) AF: 0.112 AC: 576 AN: 5162

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4816

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10568

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22536 AN: 67852

Other (OTH) AF: 0.320 AC: 676 AN: 2112

Alfa AF: 0.330 Hom.: 7190

Bravo AF: 0.331

Asia WGS AF: 0.232 AC: 804 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	0.24
DANN	Benign	0.32
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9319110;

hg19: chr13-85612388;