8-53497648-G-A

Variant names:

• chr8-53497648-G-A
• rs10958369
• ENST00000656976.1:n.880-2030C>T

Variant summary

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

The ENST00000656976.1(LINC02984):​n.880-2030C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,982 control chromosomes in the GnomAD database, including 14,858 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 0.41 (14858 hom., cov: 31)
• Consequence: LINC02984 ENST00000656976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901947	XR_007060913.1	n.145+13416G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02984	ENST00000656976.1	n.880-2030C>T		intron_variant	Intron 2 of 3
LINC02984	ENST00000834748.1	n.630+25681C>T		intron_variant	Intron 1 of 3
LINC02984	ENST00000834749.1	n.636+25681C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62471 AN: 151864 Hom.: 14866 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.411 AC: 62471 AN: 151982 Hom.: 14858 Cov.: 31 AF XY: 0.405 AC XY: 30074 AN XY: 74294

African (AFR) AF: 0.177 AC: 7332 AN: 41502

American (AMR) AF: 0.384 AC: 5868 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1934 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2165 AN: 5136

South Asian (SAS) AF: 0.283 AC: 1356 AN: 4796

European-Finnish (FIN) AF: 0.473 AC: 4996 AN: 10554

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37423 AN: 67938

Other (OTH) AF: 0.454 AC: 957 AN: 2106

Alfa AF: 0.520 Hom.: 44870

Bravo AF: 0.400

Asia WGS AF: 0.349 AC: 1215 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	1.3
DANN	Benign	0.42
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs10958369; hg19: chr8-54410208; COSMIC: COSV63295436;