ENST00000519786.1:n.116-2623C>T

Variant names:

• chr8-119433646-G-A
• rs10505360
• ENST00000519786.1:n.116-2623C>T

Variant summary

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

The ENST00000519786.1(ENSG00000253398):​n.116-2623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 152,126 control chromosomes in the GnomAD database, including 1,308 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 0.080 (1308 hom., cov: 32)
• Consequence: ENSG00000253398 ENST00000519786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

ENSG00000253398 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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
ENSG00000253398	ENST00000519786.1	n.116-2623C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12189 AN: 152008 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0803 AC: 12217 AN: 152126 Hom.: 1308 Cov.: 32 AF XY: 0.0771 AC XY: 5738 AN XY: 74404

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0440 Hom.: 116

Bravo AF: 0.0901

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505360; hg19: chr8-120445886;