ENST00000519041.1:n.449-710A>T

Variant names:

• chr8-86760126-A-T
• rs9332439
• ENST00000519041.1:n.449-710A>T

Variant summary

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

The ENST00000519041.1(ENSG00000253778):​n.449-710A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,084 control chromosomes in the GnomAD database, including 24,778 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 0.56 (24778 hom., cov: 32)
• Consequence: ENSG00000253778 ENST00000519041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 0 publications found

Genes affected

ENSG00000253778 (HGNC:58258):

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 (AFR) allele frequency at 95% confidence interval = 0.708 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
ENSG00000253778	ENST00000519041.1	n.449-710A>T		intron_variant	Intron 1 of 2	3
ENSG00000253778	ENST00000805695.1	n.380-12170A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85465 AN: 151966 Hom.: 24766 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.562 AC: 85525 AN: 152084 Hom.: 24778 Cov.: 32 AF XY: 0.563 AC XY: 41837 AN XY: 74328

African (AFR) AF: 0.715 AC: 29673 AN: 41498

American (AMR) AF: 0.541 AC: 8266 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2673 AN: 5170

South Asian (SAS) AF: 0.499 AC: 2405 AN: 4824

European-Finnish (FIN) AF: 0.522 AC: 5514 AN: 10556

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33809 AN: 67968

Other (OTH) AF: 0.522 AC: 1104 AN: 2114

Alfa AF: 0.547 Hom.: 2872

Bravo AF: 0.568

Asia WGS AF: 0.510 AC: 1776 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	1.8
DANN	Benign	0.85
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9332439; hg19: chr8-87772354;