rs10518306

chr4-123815050-C-T

Variant summary

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

The NR_027105.3(LINC01091):n.537-14045C>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 0.0931 in 152,088 control chromosomes in the GnomAD database, including 763 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 0.093 (763 hom., cov: 32)
• Consequence: LINC01091 NR_027105.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01091	NR_027105.3	n.537-14045C>T		intron_variant, non_coding_transcript_variant
LINC01091	NR_027106.2	n.113-14045C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01091	ENST00000664622.1	n.509-14045C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14144 AN: 151968 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0931 AC: 14152 AN: 152088 Hom.: 763 Cov.: 32 AF XY: 0.0922 AC XY: 6854 AN XY: 74348

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.111

Alfa AF: 0.104 Hom.: 188

Bravo AF: 0.0867

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518306; hg19: chr4-124736205;