rs11596456

Positions:

• chr10-118812734-G-A

Variant summary

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

The ENST00000663084.1(LINC03036):​n.397-25692C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,082 control chromosomes in the GnomAD database, including 1,306 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 0.13 (1306 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

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 (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03036	ENST00000663084.1	n.397-25692C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19337 AN: 151964 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.127 AC: 19345 AN: 152082 Hom.: 1306 Cov.: 32 AF XY: 0.127 AC XY: 9451 AN XY: 74318

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.150

Alfa AF: 0.137 Hom.: 3100

Bravo AF: 0.128

Asia WGS AF: 0.157 AC: 546 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	1.9
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596456; hg19: chr10-120572246;