rs11596456

Variant names:

• chr10-118812734-G-A
• rs11596456
• ENST00000663084.1:n.397-25692C>T

Variant summary

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

The ENST00000663084.1(LINC03036):​n.397-25692C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 2 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=-0.92).
• 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 rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.424-25692C>T		intron_variant	Intron 3 of 3
LINC03036	NR_186541.1	n.500-25692C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.397-25692C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.103 AC: 4271 AN: 41484

American (AMR) AF: 0.115 AC: 1754 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3466

East Asian (EAS) AF: 0.177 AC: 913 AN: 5156

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4802

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10572

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8987 AN: 68000

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.135 Hom.: 4792

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11596456; hg19: chr10-120572246;