rs4690560

Variant names:

• chr4-177741756-G-A
• rs4690560
• ENST00000507870.1:n.374+9277G>A

Variant summary

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

The ENST00000507870.1(LINC01098):​n.374+9277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,926 control chromosomes in the GnomAD database, including 33,758 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 0.66 (33758 hom., cov: 31)
• Consequence: LINC01098 ENST00000507870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 4 publications found

Genes affected

LINC01098 (HGNC:27731): (long intergenic non-protein coding RNA 1098)

LINC01099 (HGNC:49222): (long intergenic non-protein coding RNA 1099)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01098	NR_028342.1	n.374+9277G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01098	ENST00000507870.1	n.374+9277G>A		intron_variant	Intron 2 of 5	1
LINC01099	ENST00000507011.1	n.486-12092C>T		intron_variant	Intron 4 of 4	5
LINC01098	ENST00000666825.1	n.374+9277G>A		intron_variant	Intron 2 of 2
LINC01099	ENST00000798945.1	n.593+14988C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100479 AN: 151808 Hom.: 33743 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.662 AC: 100539 AN: 151926 Hom.: 33758 Cov.: 31 AF XY: 0.663 AC XY: 49251 AN XY: 74254

African (AFR) AF: 0.552 AC: 22864 AN: 41428

American (AMR) AF: 0.600 AC: 9126 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3944 AN: 5134

South Asian (SAS) AF: 0.582 AC: 2804 AN: 4820

European-Finnish (FIN) AF: 0.725 AC: 7650 AN: 10556

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49062 AN: 67980

Other (OTH) AF: 0.693 AC: 1466 AN: 2114

Alfa AF: 0.704 Hom.: 163365

Bravo AF: 0.649

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4690560; hg19: chr4-178662910;