rs688709

Positions:

• chr15-47791186-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01491 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.47791186A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000651940.1	n.500T>C		non_coding_transcript_exon_variant	6/7
LINC01491	ENST00000653152.1	n.540T>C		non_coding_transcript_exon_variant	6/7
LINC01491	ENST00000654238.1	n.515T>C		non_coding_transcript_exon_variant	6/7

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

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.298

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs688709; hg19: chr15-48083383;