13-63060217-G-T

Variant names:

• chr13-63060217-G-T
• rs9317284
• ENST00000618134.1:n.177+7809G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000618134.1(ENSG00000273550):​n.177+7809G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 151,016 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.052 (0 hom., cov: 60)
• Consequence: ENSG00000273550 ENST00000618134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

ENSG00000273550 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0686 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
ENSG00000273550	ENST00000618134.1	n.177+7809G>T		intron_variant	Intron 2 of 2	3
ENSG00000273550	ENST00000658907.1	n.82+25185G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0525 AC: 7917 AN: 150898 Hom.: 0 Cov.: 60

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0638

Gnomad ASJ AF: 0.0659

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0524 AC: 7911 AN: 151016 Hom.: 0 Cov.: 60 AF XY: 0.0532 AC XY: 3929 AN XY: 73796

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0637

Gnomad4 ASJ AF: 0.0659

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0880

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.114 Hom.: 139

Bravo AF: 0.0944

Asia WGS AF: 0.0690 AC: 239 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317284; hg19: chr13-63634350;