10-118836909-T-C

Variant names:

• chr10-118836909-T-C
• rs7091672
• ENST00000663084.1:n.396+29278A>G

Variant summary

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

The ENST00000663084.1(LINC03036):​n.396+29278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,126 control chromosomes in the GnomAD database, including 29,838 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 0.62 (29838 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 3 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 = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.423+29278A>G		intron_variant	Intron 3 of 3
LINC03036	NR_186541.1	n.499+29278A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.396+29278A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94667 AN: 152008 Hom.: 29816 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.623 AC: 94735 AN: 152126 Hom.: 29838 Cov.: 32 AF XY: 0.628 AC XY: 46717 AN XY: 74354

African (AFR) AF: 0.524 AC: 21720 AN: 41488

American (AMR) AF: 0.656 AC: 10011 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3096 AN: 5176

South Asian (SAS) AF: 0.631 AC: 3043 AN: 4820

European-Finnish (FIN) AF: 0.757 AC: 8007 AN: 10584

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44302 AN: 68006

Other (OTH) AF: 0.638 AC: 1346 AN: 2110

Alfa AF: 0.634 Hom.: 32325

Bravo AF: 0.616

Asia WGS AF: 0.598 AC: 2079 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	0.87
DANN	Benign	0.72
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs7091672; hg19: chr10-120596421;