ENST00000663084.1:n.201-182C>T

Variant names:

• chr10-119026042-G-A
• rs7905458
• ENST00000437838.2:n.34-182C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663084.1(LINC03036):​n.201-182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,112 control chromosomes in the GnomAD database, including 23,486 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 0.55 (23486 hom., cov: 33)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 2 publications found

Genes affected

LINC03036 (HGNC:56220): (long intergenic non-protein coding RNA 3036)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663084.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	NR_186540.1		n.228-182C>T		intron	N/A
	LINC03036	NR_186541.1		n.228-182C>T		intron	N/A
	LINC03036	NR_186542.1		n.228-182C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000437838.2	TSL:3	n.34-182C>T		intron	N/A
	LINC03036	ENST00000663084.1		n.201-182C>T		intron	N/A
	LINC03036	ENST00000762832.1		n.115+117C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83338 AN: 151994 Hom.: 23474 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.548 AC: 83379 AN: 152112 Hom.: 23486 Cov.: 33 AF XY: 0.552 AC XY: 41034 AN XY: 74354

African (AFR) AF: 0.426 AC: 17681 AN: 41498

American (AMR) AF: 0.617 AC: 9438 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2590 AN: 5176

South Asian (SAS) AF: 0.661 AC: 3193 AN: 4830

European-Finnish (FIN) AF: 0.581 AC: 6146 AN: 10570

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39795 AN: 67966

Other (OTH) AF: 0.592 AC: 1247 AN: 2108

Alfa AF: 0.547 Hom.: 2887

Bravo AF: 0.542

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs7905458; hg19: chr10-120785554;