chr1-58891154-T-C

Position:

• chr1-58891154-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.156-2391T>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 0.332 in 151,936 control chromosomes in the GnomAD database, including 8,728 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 0.33 (8728 hom., cov: 31)
• Consequence: LINC01135 NR_034014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

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

LINC02777 (HGNC:54297): (long intergenic non-protein coding RNA 2777)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01135	NR_034014.1	n.156-2391T>C		intron_variant, non_coding_transcript_variant
LINC02777	NR_183655.1	n.737-1946A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01135	ENST00000649834.1	n.179-5103T>C		intron_variant, non_coding_transcript_variant
LINC02777	ENST00000665413.1	n.291+4691A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50448 AN: 151818 Hom.: 8729 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.332 AC: 50465 AN: 151936 Hom.: 8728 Cov.: 31 AF XY: 0.335 AC XY: 24914 AN XY: 74276

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.357

Alfa AF: 0.341 Hom.: 5058

Bravo AF: 0.342

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6661505; hg19: chr1-59356826;