rs1384804

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-78659987-C-A
• chr8-78659987-C-G
• chr8-78659987-C-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.

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.1011+5018G>T		intron	N/A
	ENSG00000286675	ENST00000721158.1		n.978+5018G>T		intron	N/A
	ENSG00000286675	ENST00000721159.1		n.978+5018G>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs1384804;

hg19: chr8-79572222;