8-8719583-T-C

Variant names:

• chr8-8719583-T-C
• rs4841017
• ENST00000641764.1:n.-47A>G

Variant summary

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

The ENST00000641764.1(ENSG00000284717):​n.-47A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,052 control chromosomes in the GnomAD database, including 5,877 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 0.27 (5876 hom., cov: 32)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: ENSG00000284717 ENST00000641764.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

Genes affected

ENSG00000284717 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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
ENSG00000284717	ENST00000641764.1	n.-47A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41026 AN: 151918 Hom.: 5862 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.270 AC: 41074 AN: 152034 Hom.: 5876 Cov.: 32 AF XY: 0.278 AC XY: 20646 AN XY: 74308

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.259

Alfa AF: 0.259 Hom.: 1048

Bravo AF: 0.265

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4841017; hg19: chr8-8577093;