rs989980

Variant names:

• chr9-106467756-C-T
• rs989980
• ENST00000425709.3:n.170+16868C>T

Variant summary

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

The ENST00000425709.3(LINC01505):​n.170+16868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,930 control chromosomes in the GnomAD database, including 22,189 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 0.53 (22189 hom., cov: 32)
• Consequence: LINC01505 ENST00000425709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

Genes affected

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

LOC107987108 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425709.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01505	ENST00000425709.3	TSL:1	n.170+16868C>T		intron	N/A
	LINC01505	ENST00000411451.3	TSL:3	n.74+16868C>T		intron	N/A
	LINC01505	ENST00000435485.5	TSL:5	n.172-31731C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80097 AN: 151812 Hom.: 22125 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.528 AC: 80231 AN: 151930 Hom.: 22189 Cov.: 32 AF XY: 0.523 AC XY: 38813 AN XY: 74234

African (AFR) AF: 0.697 AC: 28913 AN: 41454

American (AMR) AF: 0.529 AC: 8070 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1621 AN: 5150

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4497 AN: 10546

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.467 AC: 31744 AN: 67928

Other (OTH) AF: 0.513 AC: 1084 AN: 2112

Alfa AF: 0.486 Hom.: 30963

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.010

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: rs989980;

hg19: chr9-109230037;