rs7552624

chr1-58847764-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.156-45781T>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 0.233 in 152,128 control chromosomes in the GnomAD database, including 4,753 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 0.23 (4753 hom., cov: 32)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

Genes affected

(HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01135	NR_034014.1	n.156-45781T>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_034015.1	n.156-45781T>C		intron_variant, non_coding_transcript_variant
LINC01135	NR_108106.1	n.156-51283T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000424592.1	n.31+3460A>G		intron_variant, non_coding_transcript_variant		3
LINC01135	ENST00000649834.1	n.179-48493T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35378 AN: 152010 Hom.: 4752 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.233 AC: 35390 AN: 152128 Hom.: 4753 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74368

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.254

Alfa AF: 0.244 Hom.: 1100

Bravo AF: 0.225

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
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: rs7552624; hg19: chr1-59313436;