rs2716140

chr1-59006725-A-C

Variant summary

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

The ENST00000634502.1(LINC01358):n.397-13770A>C 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 0.435 in 152,024 control chromosomes in the GnomAD database, including 14,879 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 0.44 (14879 hom., cov: 32)
• Consequence: LINC01358 ENST00000634502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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 = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01358	ENST00000634502.1	n.397-13770A>C		intron_variant, non_coding_transcript_variant		5
LINC01358	ENST00000662532.1	n.176+52806A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66104 AN: 151906 Hom.: 14868 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.435 AC: 66151 AN: 152024 Hom.: 14879 Cov.: 32 AF XY: 0.431 AC XY: 31999 AN XY: 74300

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.445

Alfa AF: 0.407 Hom.: 17435

Bravo AF: 0.433

Asia WGS AF: 0.268 AC: 931 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	1.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2716140; hg19: chr1-59472397;