8-53508661-A-G

Variant names:

• chr8-53508661-A-G
• rs1477958
• ENST00000656976.1:n.879+8051T>C

Variant summary

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

The ENST00000656976.1(LINC02984):​n.879+8051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,168 control chromosomes in the GnomAD database, including 47,584 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 0.79 (47584 hom., cov: 32)
• Consequence: LINC02984 ENST00000656976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 0 publications found

Genes affected

LINC02984 (HGNC:56063): (long intergenic non-protein coding RNA 2984)

ENSG00000308573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656976.1. 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
	LINC02984	ENST00000656976.1		n.879+8051T>C		intron	N/A
	LINC02984	ENST00000834748.1		n.630+14668T>C		intron	N/A
	LINC02984	ENST00000834749.1		n.636+14668T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119823 AN: 152050 Hom.: 47550 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.788 AC: 119914 AN: 152168 Hom.: 47584 Cov.: 32 AF XY: 0.786 AC XY: 58503 AN XY: 74386

African (AFR) AF: 0.862 AC: 35775 AN: 41518

American (AMR) AF: 0.835 AC: 12780 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2687 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4617 AN: 5174

South Asian (SAS) AF: 0.813 AC: 3918 AN: 4820

European-Finnish (FIN) AF: 0.677 AC: 7158 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50486 AN: 67980

Other (OTH) AF: 0.804 AC: 1700 AN: 2114

Alfa AF: 0.760 Hom.: 163639

Bravo AF: 0.804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.44
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: rs1477958;

hg19: chr8-54421221;