9-102578059-C-A

Position:

• chr9-102578059-C-A

Variant summary

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

The NR_103830.1(LINC00587):​n.73-212C>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 0.0635 in 152,116 control chromosomes in the GnomAD database, including 347 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 0.063 (347 hom., cov: 32)
• Consequence: LINC00587 NR_103830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

LINC00587 (HGNC:31372): (long intergenic non-protein coding RNA 587)

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 (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00587	NR_103830.1	n.73-212C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00587	ENST00000374801.3	n.74-212C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9638 AN: 151998 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0635 AC: 9655 AN: 152116 Hom.: 347 Cov.: 32 AF XY: 0.0655 AC XY: 4872 AN XY: 74352

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0688

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0665

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0435 Hom.: 47

Bravo AF: 0.0631

Asia WGS AF: 0.0950 AC: 329 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	0.32
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930551; hg19: chr9-105340341;