rs338732

Variant names:

• chr13-88390493-A-C
• rs338732

Your query was ambiguous. Multiple possible variants found:

• chr13-88390493-A-C
• chr13-88390493-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.264 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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.253

Alfa AF: 0.267 Hom.: 2013

Bravo AF: 0.252

Asia WGS AF: 0.352 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs338732; hg19: chr13-89042748;