8-8719583-T-C

Variant names:

• chr8-8719583-T-C
• rs4841017
• ENST00000765578.1:n.660+3947A>G

Variant summary

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

The ENST00000765578.1(ENSG00000254367):​n.660+3947A>G variant causes a intron 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: ENSG00000254367 ENST00000765578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 6 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254367	ENST00000765578.1		n.660+3947A>G		intron	N/A
	ENSG00000254367	ENST00000765579.1		n.741-53A>G		intron	N/A
	ENSG00000284717	ENST00000641764.1		n.-47A>G		upstream_gene	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 4 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.233 AC: 9676 AN: 41468

American (AMR) AF: 0.309 AC: 4723 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2267 AN: 5170

South Asian (SAS) AF: 0.397 AC: 1910 AN: 4808

European-Finnish (FIN) AF: 0.348 AC: 3672 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17154 AN: 67964

Other (OTH) AF: 0.259 AC: 547 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4841017; hg19: chr8-8577093;