rs9545740

Variant names:

• chr13-81501457-G-A
• rs9545740

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 0.499 in 151,742 control chromosomes in the GnomAD database, including 21,338 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 0.50 (21338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.499 AC: 75706 AN: 151622 Hom.: 21300 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.499 AC: 75786 AN: 151742 Hom.: 21338 Cov.: 32 AF XY: 0.491 AC XY: 36403 AN XY: 74154

African (AFR) AF: 0.769 AC: 31853 AN: 41434

American (AMR) AF: 0.448 AC: 6829 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3464

East Asian (EAS) AF: 0.173 AC: 895 AN: 5164

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4056 AN: 10436

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28733 AN: 67884

Other (OTH) AF: 0.461 AC: 968 AN: 2100

Alfa AF: 0.442 Hom.: 25800

Bravo AF: 0.516

Asia WGS AF: 0.213 AC: 738 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.47
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs9545740; hg19: chr13-82075592;