1-58859954-T-C

Position:

• chr1-58859954-T-C

Variant summary

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

The NR_034014.1(LINC01135):​n.156-33591T>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 0.0599 in 152,290 control chromosomes in the GnomAD database, including 373 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 0.060 (373 hom., cov: 32)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01135	NR_034014.1	n.156-33591T>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_034015.1	n.156-33591T>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_108106.1	n.156-39093T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01135	ENST00000649834.1	n.179-36303T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9105 AN: 152172 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0599 AC: 9120 AN: 152290 Hom.: 373 Cov.: 32 AF XY: 0.0638 AC XY: 4749 AN XY: 74466

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0250

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0314 Hom.: 295

Bravo AF: 0.0592

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.64
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4601609; hg19: chr1-59325626;