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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661869.2. 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
	ENSG00000286675	ENST00000661869.2		n.1012-12813G>C		intron	N/A
	ENSG00000286675	ENST00000721158.1		n.979-12813G>C		intron	N/A
	ENSG00000286675	ENST00000721159.1		n.979-12813G>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1466526;

hg19: chr8-79555474;