10-118867050-A-G

Variant names:

• chr10-118867050-A-G
• rs10510050
• ENST00000663084.1:n.265-732T>C

Variant summary

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

The ENST00000663084.1(LINC03036):​n.265-732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,948 control chromosomes in the GnomAD database, including 21,329 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 0.52 (21329 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.292-732T>C		intron_variant	Intron 2 of 3
LINC03036	NR_186541.1	n.368-732T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.265-732T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79532 AN: 151830 Hom.: 21322 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.524 AC: 79565 AN: 151948 Hom.: 21329 Cov.: 32 AF XY: 0.530 AC XY: 39390 AN XY: 74266

African (AFR) AF: 0.405 AC: 16752 AN: 41402

American (AMR) AF: 0.580 AC: 8867 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3104 AN: 5166

South Asian (SAS) AF: 0.536 AC: 2578 AN: 4810

European-Finnish (FIN) AF: 0.656 AC: 6924 AN: 10550

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37471 AN: 67952

Other (OTH) AF: 0.527 AC: 1111 AN: 2110

Alfa AF: 0.540 Hom.: 45329

Bravo AF: 0.518

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10510050; hg19: chr10-120626562;