10-118856240-A-G

Variant names:

• chr10-118856240-A-G
• rs1409314
• ENST00000663084.1:n.396+9947T>C

Variant summary

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

The ENST00000663084.1(LINC03036):​n.396+9947T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,970 control chromosomes in the GnomAD database, including 19,135 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 0.50 (19135 hom., cov: 31)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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+9947T>C		intron	N/A
	LINC03036	NR_186541.1		n.499+9947T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000663084.1		n.396+9947T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75867 AN: 151852 Hom.: 19126 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.500 AC: 75914 AN: 151970 Hom.: 19135 Cov.: 31 AF XY: 0.505 AC XY: 37489 AN XY: 74278

African (AFR) AF: 0.430 AC: 17807 AN: 41426

American (AMR) AF: 0.544 AC: 8305 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3464

East Asian (EAS) AF: 0.564 AC: 2901 AN: 5146

South Asian (SAS) AF: 0.508 AC: 2447 AN: 4820

European-Finnish (FIN) AF: 0.593 AC: 6271 AN: 10578

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34650 AN: 67954

Other (OTH) AF: 0.491 AC: 1035 AN: 2108

Alfa AF: 0.501 Hom.: 24602

Bravo AF: 0.498

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs1409314; hg19: chr10-120615752;