rs11190141

Variant names:

• chr10-99532633-C-T
• rs11190141
• ENST00000795233.1:n.135G>A

Variant summary

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

The ENST00000795233.1(LINC01475):​n.135G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,088 control chromosomes in the GnomAD database, including 12,526 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 0.40 (12526 hom., cov: 33)
• Consequence: LINC01475 ENST00000795233.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 18 publications found

Genes affected

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01475	ENST00000795233.1	n.135G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC01475	ENST00000795234.1	n.149G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61037 AN: 151970 Hom.: 12499 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.402 AC: 61113 AN: 152088 Hom.: 12526 Cov.: 33 AF XY: 0.407 AC XY: 30270 AN XY: 74354

African (AFR) AF: 0.409 AC: 16973 AN: 41478

American (AMR) AF: 0.452 AC: 6904 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2748 AN: 5184

South Asian (SAS) AF: 0.372 AC: 1793 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4746 AN: 10568

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25775 AN: 67980

Other (OTH) AF: 0.372 AC: 784 AN: 2110

Alfa AF: 0.391 Hom.: 19885

Bravo AF: 0.404

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.26
PromoterAI		-0.0010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11190141; hg19: chr10-101292390;