rs16960195

Variant names:

• chr15-47834032-A-G
• rs16960195
• ENST00000558434.2:n.261-6416T>C

Variant summary

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

The ENST00000558434.2(LINC01491):​n.261-6416T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,230 control chromosomes in the GnomAD database, including 2,682 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 0.17 (2682 hom., cov: 33)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 0 publications found

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558434.2. 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
	LINC01491	NR_120336.1		n.237-6416T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558434.2	TSL:3	n.261-6416T>C		intron	N/A
	LINC01491	ENST00000558792.6	TSL:3	n.251-6416T>C		intron	N/A
	LINC01491	ENST00000561238.3	TSL:3	n.273-6416T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26076 AN: 152112 Hom.: 2676 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.171 AC: 26104 AN: 152230 Hom.: 2682 Cov.: 33 AF XY: 0.169 AC XY: 12545 AN XY: 74446

African (AFR) AF: 0.268 AC: 11133 AN: 41522

American (AMR) AF: 0.151 AC: 2308 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5188

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1075 AN: 10618

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9885 AN: 68004

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.168 Hom.: 535

Bravo AF: 0.180

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.31
PhyloP100		-0.29

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: rs16960195;

hg19: chr15-48126229;