rs9545255

chr13-35755150-G-C

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 0.452 in 152,130 control chromosomes in the GnomAD database, including 19,114 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 0.45 (19114 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68806 AN: 152012 Hom.: 19106 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.452 AC: 68830 AN: 152130 Hom.: 19114 Cov.: 33 AF XY: 0.455 AC XY: 33858 AN XY: 74364

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.498

Alfa AF: 0.528 Hom.: 2966

Bravo AF: 0.431

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.49
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9545255; hg19: chr13-36329287;