rs688709

Variant names:

• chr15-47791186-A-G
• rs688709
• ENST00000651940.1:n.500T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000651940.1(LINC01491):​n.500T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,076 control chromosomes in the GnomAD database, including 6,992 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 0.27 (6992 hom., cov: 32)
• Consequence: LINC01491 ENST00000651940.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000651940.1	n.500T>C		non_coding_transcript_exon_variant	Exon 6 of 7
LINC01491	ENST00000653152.1	n.540T>C		non_coding_transcript_exon_variant	Exon 6 of 7
LINC01491	ENST00000654238.1	n.515T>C		non_coding_transcript_exon_variant	Exon 6 of 7

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40895 AN: 151958 Hom.: 6993 Cov.: 32

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.269 AC: 40881 AN: 152076 Hom.: 6992 Cov.: 32 AF XY: 0.261 AC XY: 19366 AN XY: 74330

African (AFR) AF: 0.0730 AC: 3029 AN: 41508

American (AMR) AF: 0.318 AC: 4854 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1244 AN: 3472

East Asian (EAS) AF: 0.160 AC: 829 AN: 5168

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4822

European-Finnish (FIN) AF: 0.246 AC: 2600 AN: 10550

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25830 AN: 67954

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.309 Hom.: 1394

Bravo AF: 0.268

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs688709; hg19: chr15-48083383;