rs4598514

chr1-59053946-T-G

Variant summary

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

The NR_110626.2(LINC01358):n.238+32369T>G 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 0.246 in 152,210 control chromosomes in the GnomAD database, including 4,941 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 0.25 (4941 hom., cov: 33)
• Consequence: LINC01358 NR_110626.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LINC01358 (HGNC:50589): (long intergenic non-protein coding RNA 1358)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01358	NR_110626.2	n.238+32369T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01358	ENST00000634502.1	n.1883-2745T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37428 AN: 152092 Hom.: 4931 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.246 AC: 37460 AN: 152210 Hom.: 4941 Cov.: 33 AF XY: 0.240 AC XY: 17901 AN XY: 74450

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.254

Alfa AF: 0.236 Hom.: 625

Bravo AF: 0.250

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.67
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4598514; hg19: chr1-59519618;