rs1454214

chr4-177779708-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_028342.1(LINC01098):n.374+47229A>T variant causes a intron, non coding transcript 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 NR_028342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01098	NR_028342.1	n.374+47229A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01099	ENST00000507011.1	n.120-3114T>A		intron_variant, non_coding_transcript_variant		5
LINC01098	ENST00000507870.1	n.374+47229A>T		intron_variant, non_coding_transcript_variant		1
LINC01098	ENST00000666825.1	n.374+47229A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.207

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454214; hg19: chr4-178700862;