rs1394615

Variant names:

• chr5-175088629-G-A
• rs1394615
• ENST00000798224.1:n.56+17667C>T

Variant summary

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

The ENST00000798224.1(LINC01951):​n.56+17667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,790 control chromosomes in the GnomAD database, including 20,831 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 0.51 (20831 hom., cov: 31)
• Consequence: LINC01951 ENST00000798224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 1 publications found

Genes affected

LINC01951 (HGNC:52774): (long intergenic non-protein coding RNA 1951)

LOC107986484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798224.1. 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
	LINC01951	ENST00000798224.1		n.56+17667C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76850 AN: 151672 Hom.: 20825 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76874 AN: 151790 Hom.: 20831 Cov.: 31 AF XY: 0.509 AC XY: 37742 AN XY: 74132

African (AFR) AF: 0.298 AC: 12352 AN: 41412

American (AMR) AF: 0.513 AC: 7822 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2029 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2153 AN: 5130

South Asian (SAS) AF: 0.598 AC: 2872 AN: 4800

European-Finnish (FIN) AF: 0.657 AC: 6896 AN: 10504

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.604 AC: 41007 AN: 67934

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.568 Hom.: 42832

Bravo AF: 0.483

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.68
PhyloP100		-0.41

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: rs1394615;

hg19: chr5-174515632;

COSMIC: COSV60235536;