8-78659987-C-A

Variant names:

• chr8-78659987-C-A
• rs1384804
• ENST00000661869.2:n.1011+5018G>T

Variant summary

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

The ENST00000661869.2(ENSG00000286675):​n.1011+5018G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,968 control chromosomes in the GnomAD database, including 36,360 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 0.68 (36360 hom., cov: 33)
• Consequence: ENSG00000286675 ENST00000661869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 18 publications found

Genes affected

ENSG00000286675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375911	XR_007060972.1	n.975+5018G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286675	ENST00000661869.2	n.1011+5018G>T		intron_variant	Intron 1 of 1
ENSG00000286675	ENST00000721158.1	n.978+5018G>T		intron_variant	Intron 1 of 2
ENSG00000286675	ENST00000721159.1	n.978+5018G>T		intron_variant	Intron 1 of 2
ENSG00000286675	ENST00000721160.1	n.351+5018G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103831 AN: 151850 Hom.: 36342 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.684 AC: 103894 AN: 151968 Hom.: 36360 Cov.: 33 AF XY: 0.686 AC XY: 50934 AN XY: 74284

African (AFR) AF: 0.531 AC: 21992 AN: 41448

American (AMR) AF: 0.749 AC: 11416 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4686 AN: 5170

South Asian (SAS) AF: 0.760 AC: 3655 AN: 4812

European-Finnish (FIN) AF: 0.739 AC: 7814 AN: 10574

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.737 AC: 50076 AN: 67938

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.716 Hom.: 72421

Bravo AF: 0.681

Asia WGS AF: 0.792 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1384804; hg19: chr8-79572222;