rs1853432

chr1-58849530-A-T

Variant summary

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

The NR_034014.1(LINC01135):n.156-44015A>T 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 0.753 in 152,248 control chromosomes in the GnomAD database, including 43,484 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 0.75 (43484 hom., cov: 33)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01135	NR_034014.1	n.156-44015A>T		intron_variant, non_coding_transcript_variant
LINC01135	NR_034015.1	n.156-44015A>T		intron_variant, non_coding_transcript_variant
LINC01135	NR_108106.1	n.156-49517A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000424592.1	n.31+1694T>A		intron_variant, non_coding_transcript_variant		3
LINC01135	ENST00000649834.1	n.179-46727A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114493 AN: 152130 Hom.: 43434 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.753 AC: 114598 AN: 152248 Hom.: 43484 Cov.: 33 AF XY: 0.745 AC XY: 55482 AN XY: 74442

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.754

Alfa AF: 0.766 Hom.: 5551

Bravo AF: 0.755

Asia WGS AF: 0.531 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.24
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1853432; hg19: chr1-59315202;