chr8-53453931-C-A

Variant names:

• chr8-53453931-C-A
• rs10429416
• ENST00000521558.2:n.135+29656G>T

Variant summary

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

The ENST00000521558.2(LINC02984):​n.135+29656G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,928 control chromosomes in the GnomAD database, including 2,138 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 0.14 (2138 hom., cov: 32)
• Consequence: LINC02984 ENST00000521558.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02984	ENST00000521558.2	n.135+29656G>T		intron_variant	Intron 1 of 4	3
LINC02984	ENST00000653042.1	n.234+29656G>T		intron_variant	Intron 1 of 6
LINC02984	ENST00000653150.3	n.404+29656G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21943 AN: 151810 Hom.: 2131 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.145 AC: 21969 AN: 151928 Hom.: 2138 Cov.: 32 AF XY: 0.142 AC XY: 10534 AN XY: 74266

African (AFR) AF: 0.273 AC: 11323 AN: 41432

American (AMR) AF: 0.105 AC: 1591 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.0793 AC: 410 AN: 5170

South Asian (SAS) AF: 0.111 AC: 535 AN: 4822

European-Finnish (FIN) AF: 0.0532 AC: 562 AN: 10568

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6405 AN: 67932

Other (OTH) AF: 0.141 AC: 297 AN: 2110

Alfa AF: 0.112 Hom.: 1109

Bravo AF: 0.153

Asia WGS AF: 0.113 AC: 394 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs10429416; hg19: chr8-54366491;