rs330700

chr1-187209585-C-Achr1-187209585-C-T

Variant summary

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

The NR_126347.1(LINC01036):n.106-93881C>A 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 0.834 in 150,820 control chromosomes in the GnomAD database, including 52,546 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 0.83 (52546 hom., cov: 27)
• Consequence: LINC01036 NR_126347.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

LINC01036 (HGNC:49024): (long intergenic non-protein coding RNA 1036)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01036	NR_126347.1	n.106-93881C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01036	ENST00000643891.1	n.804-117336C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.834 AC: 125691 AN: 150714 Hom.: 52490 Cov.: 27

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.834 AC: 125801 AN: 150820 Hom.: 52546 Cov.: 27 AF XY: 0.837 AC XY: 61635 AN XY: 73622

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.840

Alfa AF: 0.771 Hom.: 2646

Bravo AF: 0.832

Asia WGS AF: 0.784 AC: 2720 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs330700; hg19: chr1-187178717;