10-118856049-C-T

Variant names:

• chr10-118856049-C-T
• rs4752219
• ENST00000663084.1:n.396+10138G>A

Variant summary

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

The ENST00000663084.1(LINC03036):​n.396+10138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,990 control chromosomes in the GnomAD database, including 13,426 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 0.41 (13426 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	NR_186540.1		n.423+10138G>A		intron	N/A
	LINC03036	NR_186541.1		n.499+10138G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000663084.1		n.396+10138G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62063 AN: 151872 Hom.: 13428 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.408 AC: 62074 AN: 151990 Hom.: 13426 Cov.: 32 AF XY: 0.413 AC XY: 30677 AN XY: 74288

African (AFR) AF: 0.256 AC: 10627 AN: 41458

American (AMR) AF: 0.494 AC: 7554 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2175 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1872 AN: 4796

European-Finnish (FIN) AF: 0.541 AC: 5702 AN: 10542

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30996 AN: 67962

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.429 Hom.: 20561

Bravo AF: 0.404

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.43
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4752219; hg19: chr10-120615561;