10-118830191-T-C

Variant names:

• chr10-118830191-T-C
• rs1409317
• ENST00000663084.1:n.396+35996A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_186540.1(LINC03036):​n.423+35996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,998 control chromosomes in the GnomAD database, including 10,849 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 0.37 (10849 hom., cov: 31)
• Consequence: LINC03036 NR_186540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.423+35996A>G		intron_variant	Intron 3 of 3
LINC03036	NR_186541.1	n.499+35996A>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+35996A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56701 AN: 151878 Hom.: 10836 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.373 AC: 56745 AN: 151998 Hom.: 10849 Cov.: 31 AF XY: 0.372 AC XY: 27653 AN XY: 74268

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.371

Alfa AF: 0.350 Hom.: 1141

Bravo AF: 0.374

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409317; hg19: chr10-120589703;