10-118856240-A-G

Position:

• chr10-118856240-A-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+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 NR_186540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

Genes affected

LINC03036 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.423+9947T>C		intron_variant
LINC03036	NR_186541.1	n.499+9947T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.396+9947T>C		intron_variant

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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.491

Alfa AF: 0.501 Hom.: 17841

Bravo AF: 0.498

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409314; hg19: chr10-120615752;