chr13-88390493-A-C

Variant names:

• chr13-88390493-A-C
• rs338732

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 0.264 in 151,966 control chromosomes in the GnomAD database, including 5,644 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 0.26 (5644 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.264 AC: 40018 AN: 151848 Hom.: 5637 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.264 AC: 40053 AN: 151966 Hom.: 5644 Cov.: 31 AF XY: 0.266 AC XY: 19780 AN XY: 74276

African (AFR) AF: 0.203 AC: 8401 AN: 41446

American (AMR) AF: 0.195 AC: 2975 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2086 AN: 5124

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4814

European-Finnish (FIN) AF: 0.325 AC: 3439 AN: 10574

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19577 AN: 67966

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.266 Hom.: 2464

Bravo AF: 0.252

Asia WGS AF: 0.352 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs338732; hg19: chr13-89042748;