ENST00000519793.1:n.242+837C>T

Variant names:

• chr8-101451374-G-A
• rs678347
• ENST00000519793.1:n.242+837C>T

Variant summary

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

The ENST00000519793.1(ENSG00000254084):​n.242+837C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,992 control chromosomes in the GnomAD database, including 35,091 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 0.67 (35091 hom., cov: 32)
• Consequence: ENSG00000254084 ENST00000519793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

ENSG00000254084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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
ENSG00000254084	ENST00000519793.1	n.242+837C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102108 AN: 151874 Hom.: 35088 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.672 AC: 102143 AN: 151992 Hom.: 35091 Cov.: 32 AF XY: 0.671 AC XY: 49863 AN XY: 74304

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.677

Alfa AF: 0.653 Hom.: 5642

Bravo AF: 0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678347; hg19: chr8-102463602;