10-118928058-C-A

Variant names:

• chr10-118928058-C-A
• rs10787879
• ENST00000663084.1:n.265-61740G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663084.1(LINC03036):​n.265-61740G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,152 control chromosomes in the GnomAD database, including 39,567 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 0.71 (39567 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08
• Publications: 3 publications found

Genes affected

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

ENSG00000294178 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.292-61740G>T		intron_variant	Intron 2 of 3
LINC03036	NR_186541.1	n.304-6638G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.265-61740G>T		intron_variant	Intron 2 of 3
ENSG00000294178	ENST00000721698.1	n.131-6638G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108122 AN: 152034 Hom.: 39541 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.711 AC: 108199 AN: 152152 Hom.: 39567 Cov.: 32 AF XY: 0.714 AC XY: 53078 AN XY: 74374

African (AFR) AF: 0.526 AC: 21816 AN: 41498

American (AMR) AF: 0.746 AC: 11402 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2612 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4192 AN: 5176

South Asian (SAS) AF: 0.724 AC: 3496 AN: 4826

European-Finnish (FIN) AF: 0.820 AC: 8680 AN: 10584

Middle Eastern (MID) AF: 0.724 AC: 210 AN: 290

European-Non Finnish (NFE) AF: 0.788 AC: 53589 AN: 67992

Other (OTH) AF: 0.712 AC: 1506 AN: 2114

Alfa AF: 0.756 Hom.: 120746

Bravo AF: 0.701

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	17
DANN	Benign	0.69
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs10787879; hg19: chr10-120687570;