ENST00000519147.1:n.134+8543T>G

Variant names:

• chr8-8772759-A-C
• rs506960
• ENST00000519147.1:n.134+8543T>G

Variant summary

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

The ENST00000519147.1(ENSG00000254367):​n.134+8543T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,916 control chromosomes in the GnomAD database, including 10,411 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 0.35 (10411 hom., cov: 31)
• Consequence: ENSG00000254367 ENST00000519147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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
ENSG00000254367	ENST00000519147.1	n.134+8543T>G		intron_variant	Intron 1 of 2	3
ENSG00000254367	ENST00000522213.5	n.374+9347T>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53578 AN: 151798 Hom.: 10394 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53634 AN: 151916 Hom.: 10411 Cov.: 31 AF XY: 0.346 AC XY: 25682 AN XY: 74252

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.349

Alfa AF: 0.362 Hom.: 1347

Bravo AF: 0.350

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs506960; hg19: chr8-8630269;