rs13358260

Variant names:

• chr5-79549888-T-C
• rs13358260
• ENST00000799951.1:n.86+2051T>C

Variant summary

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

The ENST00000799951.1(ENSG00000304127):​n.86+2051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,198 control chromosomes in the GnomAD database, including 421 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 0.062 (421 hom., cov: 32)
• Consequence: ENSG00000304127 ENST00000799951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795
• Publications: 8 publications found

Genes affected

ENSG00000304127 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379047	XR_948497.3	n.72+2244T>C		intron_variant	Intron 1 of 2
LOC105379047	XR_948498.3	n.159+2051T>C		intron_variant	Intron 1 of 2
LOC105379047	XR_948499.3	n.167+1586T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304127	ENST00000799951.1	n.86+2051T>C		intron_variant	Intron 1 of 2
ENSG00000304127	ENST00000799952.1	n.447+2244T>C		intron_variant	Intron 1 of 2
ENSG00000304127	ENST00000799954.1	n.427+2244T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9451 AN: 152078 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0622 AC: 9464 AN: 152198 Hom.: 421 Cov.: 32 AF XY: 0.0642 AC XY: 4777 AN XY: 74402

African (AFR) AF: 0.0165 AC: 686 AN: 41550

American (AMR) AF: 0.0902 AC: 1380 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.0979 AC: 506 AN: 5170

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1382 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0695 AC: 4728 AN: 68006

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0674 Hom.: 858

Bravo AF: 0.0588

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.71
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs13358260; hg19: chr5-78845711; COSMIC: COSV50461287;