rs1454214

Variant names:

• chr4-177779708-A-T
• rs1454214
• ENST00000507870.1:n.374+47229A>T

Variant summary

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

The ENST00000507870.1(LINC01098):​n.374+47229A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,082 control chromosomes in the GnomAD database, including 4,044 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 0.21 (4044 hom., cov: 31)
• Consequence: LINC01098 ENST00000507870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01098	NR_028342.1	n.374+47229A>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01098	ENST00000507870.1	n.374+47229A>T		intron_variant	Intron 2 of 5	1
LINC01099	ENST00000507011.1	n.120-3114T>A		intron_variant	Intron 1 of 4	5
LINC01098	ENST00000666825.1	n.374+47229A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31542 AN: 151960 Hom.: 4035 Cov.: 31

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31556 AN: 152082 Hom.: 4044 Cov.: 31 AF XY: 0.209 AC XY: 15525 AN XY: 74328

African (AFR) AF: 0.0616 AC: 2559 AN: 41522

American (AMR) AF: 0.335 AC: 5117 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3464

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5150

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4816

European-Finnish (FIN) AF: 0.237 AC: 2500 AN: 10560

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17203 AN: 67976

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.229 Hom.: 549

Bravo AF: 0.207

Asia WGS AF: 0.310 AC: 1077 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		-0.051
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: rs1454214; hg19: chr4-178700862;