rs16921774

Variant names:

• chr9-102534103-C-T
• rs16921774
• ENST00000374801.3:n.73+14395C>T

Variant summary

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

The ENST00000374801.3(LINC00587):​n.73+14395C>T variant causes a intron 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 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374801.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00587	NR_103830.1		n.72+14395C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00587	ENST00000374801.3	TSL:1	n.73+14395C>T		intron	N/A

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

African (AFR) AF: 0.0747 AC: 3101 AN: 41488

American (AMR) AF: 0.0915 AC: 1395 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.173 AC: 887 AN: 5134

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4818

European-Finnish (FIN) AF: 0.0805 AC: 851 AN: 10576

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0677 AC: 4602 AN: 67962

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16921774;

hg19: chr9-105296385;