chr5-88567015-C-T

Position:

• chr5-88567015-C-T

Variant summary

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

The NR_152235.1(LINC00461):​n.219-24945G>A 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 0.0426 in 152,160 control chromosomes in the GnomAD database, including 633 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 0.043 (633 hom., cov: 32)
• Consequence: LINC00461 NR_152235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LINC00461 (HGNC:42810): (MIR9-2 host gene) This is an evolutionarily conserved gene that produces alternatively spliced long non-coding RNAs that may be expressed predominantly in the brain and visual cortex. These transcripts may be involved in tumorigenesis, as depletion by siRNA suppressed glioma cell division. Transcripts may also bind to and regulate the activity of miR-411-5p and argonaut 2, thereby altering the expression of genes involved in tumor growth. [provided by RefSeq, Nov 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00461	NR_152235.1	n.219-24945G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00461	ENST00000506978.5	n.266-24945G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6474 AN: 152042 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0426 AC: 6475 AN: 152160 Hom.: 633 Cov.: 32 AF XY: 0.0470 AC XY: 3500 AN XY: 74402

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.00462

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0281 Hom.: 30

Bravo AF: 0.0433

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977669; hg19: chr5-87862833;