8-78643239-C-G

Variant names:

• chr8-78643239-C-G
• rs1466526
• ENST00000661869.2:n.1012-12813G>C

Variant summary

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

The ENST00000661869.2(ENSG00000286675):​n.1012-12813G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,056 control chromosomes in the GnomAD database, including 38,837 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 0.71 (38837 hom., cov: 32)
• Consequence: ENSG00000286675 ENST00000661869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 11 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375911	XR_007060972.1	n.976-12813G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286675	ENST00000661869.2	n.1012-12813G>C		intron_variant	Intron 1 of 1
ENSG00000286675	ENST00000721158.1	n.979-12813G>C		intron_variant	Intron 1 of 2
ENSG00000286675	ENST00000721159.1	n.979-12813G>C		intron_variant	Intron 1 of 2
ENSG00000286675	ENST00000721160.1	n.352-12813G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107948 AN: 151940 Hom.: 38808 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.710 AC: 108023 AN: 152056 Hom.: 38837 Cov.: 32 AF XY: 0.712 AC XY: 52936 AN XY: 74322

African (AFR) AF: 0.618 AC: 25627 AN: 41452

American (AMR) AF: 0.761 AC: 11619 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1969 AN: 3462

East Asian (EAS) AF: 0.905 AC: 4691 AN: 5182

South Asian (SAS) AF: 0.779 AC: 3760 AN: 4826

European-Finnish (FIN) AF: 0.738 AC: 7798 AN: 10566

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50230 AN: 67986

Other (OTH) AF: 0.689 AC: 1456 AN: 2114

Alfa AF: 0.636 Hom.: 1863

Bravo AF: 0.712

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.40
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1466526; hg19: chr8-79555474;