rs2760501

Positions:

• chr1-58785425-T-G

Variant summary

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

The NR_034014.1(LINC01135):​n.155+120T>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 0.179 in 450,380 control chromosomes in the GnomAD database, including 16,799 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 0.28 (12126 hom., cov: 29)
  • Exomes 𝑓: 0.13 (4673 hom.)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

Genes affected

LINC01135 (HGNC:49450): (JUN divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01135	NR_034014.1	n.155+120T>G		intron_variant, non_coding_transcript_variant
LINC01135	NR_034015.1	n.155+120T>G		intron_variant, non_coding_transcript_variant
LINC01135	NR_108106.1	n.155+120T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01135	ENST00000649834.1	n.178+120T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41721 AN: 149656 Hom.: 12072 Cov.: 29

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.129 AC: 38731 AN: 300618 Hom.: 4673 AF XY: 0.129 AC XY: 22023 AN XY: 171332

Gnomad4 AFR exome AF: 0.753

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.0661

Gnomad4 EAS exome AF: 0.157

Gnomad4 SAS exome AF: 0.179

Gnomad4 FIN exome AF: 0.0954

Gnomad4 NFE exome AF: 0.0738

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.279 AC: 41831 AN: 149762 Hom.: 12126 Cov.: 29 AF XY: 0.277 AC XY: 20159 AN XY: 72810

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0958

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.240

Alfa AF: 0.110 Hom.: 4163

Bravo AF: 0.304

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760501; hg19: chr1-59251097;