rs9545255

Variant names:

• chr13-35755150-G-C
• rs9545255
• ENST00000848863.1:n.109-121C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000848863.1(ENSG00000310293):​n.109-121C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000310293 ENST00000848863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 publications found

Genes affected

ENSG00000310293 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310293	ENST00000848863.1	n.109-121C>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.139 AC: 5752 AN: 41514

American (AMR) AF: 0.563 AC: 8593 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3472

East Asian (EAS) AF: 0.179 AC: 926 AN: 5168

South Asian (SAS) AF: 0.558 AC: 2689 AN: 4816

European-Finnish (FIN) AF: 0.643 AC: 6800 AN: 10582

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40535 AN: 67982

Other (OTH) AF: 0.498 AC: 1053 AN: 2114

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9545255; hg19: chr13-36329287;