rs16921774

chr9-102534103-C-T

Variant summary

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

The NR_103830.1(LINC00587):n.72+14395C>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 0.0754 in 152,006 control chromosomes in the GnomAD database, including 439 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 0.075 (439 hom., cov: 32)
• Consequence: LINC00587 NR_103830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81

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=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00587	NR_103830.1	n.72+14395C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00587	ENST00000374801.3	n.73+14395C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11445 AN: 151888 Hom.: 439 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0754 AC: 11454 AN: 152006 Hom.: 439 Cov.: 32 AF XY: 0.0772 AC XY: 5732 AN XY: 74250

Gnomad4 AFR AF: 0.0747

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.0325

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0685 Hom.: 103

Bravo AF: 0.0753

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	18
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16921774; hg19: chr9-105296385;