rs2999131

Positions:

• chr1-58832146-G-C

Variant summary

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

The NR_034014.1(LINC01135):​n.155+46841G>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 0.407 in 152,092 control chromosomes in the GnomAD database, including 14,093 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 0.41 (14093 hom., cov: 32)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01135	NR_034014.1	n.155+46841G>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_034015.1	n.155+46841G>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_108106.1	n.155+46841G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01135	ENST00000649834.1	n.178+46841G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61873 AN: 151972 Hom.: 14062 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.407 AC: 61964 AN: 152092 Hom.: 14093 Cov.: 32 AF XY: 0.399 AC XY: 29659 AN XY: 74336

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.388

Alfa AF: 0.373 Hom.: 1462

Bravo AF: 0.430

Asia WGS AF: 0.293 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2999131; hg19: chr1-59297818;