chr13-35767531-T-G

Variant names:

• chr13-35767531-T-G
• rs9545297

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 0.209 in 152,098 control chromosomes in the GnomAD database, including 4,032 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 0.21 (4032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.209 AC: 31734 AN: 151982 Hom.: 4028 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.209 AC: 31765 AN: 152098 Hom.: 4032 Cov.: 31 AF XY: 0.210 AC XY: 15641 AN XY: 74362

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.197

Alfa AF: 0.167 Hom.: 1290

Bravo AF: 0.219

Asia WGS AF: 0.341 AC: 1189 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	3.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9545297; hg19: chr13-36341668;