rs13355565

Variant names:

• chr5-57876878-T-C
• rs13355565
• ENST00000761558.1:n.148+99T>C

Variant summary

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

The ENST00000761558.1(ENSG00000299201):​n.148+99T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,846 control chromosomes in the GnomAD database, including 2,399 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 0.14 (2399 hom., cov: 30)
• Consequence: ENSG00000299201 ENST00000761558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 0 publications found

Genes affected

ENSG00000299201 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.264 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
ENSG00000299201	ENST00000761558.1	n.148+99T>C		intron_variant	Intron 2 of 3
ENSG00000299201	ENST00000761559.1	n.52+4540T>C		intron_variant	Intron 1 of 3
ENSG00000299201	ENST00000761560.1	n.53+4540T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20977 AN: 151728 Hom.: 2370 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0795

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.139 AC: 21083 AN: 151846 Hom.: 2399 Cov.: 30 AF XY: 0.142 AC XY: 10510 AN XY: 74234

African (AFR) AF: 0.252 AC: 10394 AN: 41312

American (AMR) AF: 0.265 AC: 4042 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1418 AN: 5142

South Asian (SAS) AF: 0.115 AC: 553 AN: 4820

European-Finnish (FIN) AF: 0.0795 AC: 838 AN: 10538

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0486 AC: 3306 AN: 67992

Other (OTH) AF: 0.138 AC: 290 AN: 2104

Alfa AF: 0.135 Hom.: 416

Bravo AF: 0.162

Asia WGS AF: 0.235 AC: 815 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	3.0
DANN	Benign	0.46
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs13355565; hg19: chr5-57172705;