chr5-54684172-G-A

Variant names:

• chr5-54684172-G-A
• rs4549482
• ENST00000662448.1:n.1714-7788G>A

Variant summary

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

The ENST00000662448.1(ENSG00000287367):​n.1714-7788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,098 control chromosomes in the GnomAD database, including 47,032 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 0.77 (47032 hom., cov: 33)
• Consequence: ENSG00000287367 ENST00000662448.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

Genes affected

ENSG00000287367 (HGNC:):

LINC02998 (HGNC:56114): (long intergenic non-protein coding RNA 2998)

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 = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02998	NR_104658.1	n.401-17997C>T		intron_variant	Intron 1 of 2
LINC02998	NR_104659.1	n.159-17997C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287367	ENST00000662448.1	n.1714-7788G>A		intron_variant	Intron 2 of 5
ENSG00000305702	ENST00000812507.1	n.330-17997C>T		intron_variant	Intron 1 of 2
ENSG00000305702	ENST00000812508.1	n.571-23712C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117486 AN: 151980 Hom.: 47012 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.773 AC: 117547 AN: 152098 Hom.: 47032 Cov.: 33 AF XY: 0.777 AC XY: 57828 AN XY: 74386

African (AFR) AF: 0.545 AC: 22552 AN: 41408

American (AMR) AF: 0.780 AC: 11910 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2778 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4384 AN: 5180

South Asian (SAS) AF: 0.851 AC: 4108 AN: 4828

European-Finnish (FIN) AF: 0.946 AC: 10031 AN: 10600

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59159 AN: 68028

Other (OTH) AF: 0.781 AC: 1650 AN: 2114

Alfa AF: 0.839 Hom.: 109453

Bravo AF: 0.749

Asia WGS AF: 0.845 AC: 2939 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	5.5
DANN	Benign	0.76
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4549482; hg19: chr5-53980001; COSMIC: COSV60133099;