rs17095819

Variant names:

• chr14-59177243-A-G
• rs17095819
• ENST00000657369.1:n.716-6420A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-59177243-A-G
• chr14-59177243-A-T

Variant summary

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

The ENST00000657369.1(LINC01500):​n.716-6420A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,210 control chromosomes in the GnomAD database, including 2,355 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 (2355 hom., cov: 32)
• Consequence: LINC01500 ENST00000657369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 5 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

LOC107984642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657369.1. 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
	LINC01500	ENST00000657369.1		n.716-6420A>G		intron	N/A
	LINC01500	ENST00000663641.1		n.830-6420A>G		intron	N/A
	LINC01500	ENST00000665985.1		n.693-6420A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25289 AN: 152094 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.166 AC: 25327 AN: 152210 Hom.: 2355 Cov.: 32 AF XY: 0.163 AC XY: 12112 AN XY: 74430

African (AFR) AF: 0.225 AC: 9336 AN: 41502

American (AMR) AF: 0.118 AC: 1809 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3472

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5192

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10915 AN: 68006

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.105 Hom.: 203

Bravo AF: 0.167

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.35
PhyloP100		0.44

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: rs17095819;

hg19: chr14-59643961;