chr14-59177243-A-G

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984642	XR_001750928.1	n.42-6420A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000657369.1	n.716-6420A>G		intron_variant	Intron 5 of 5
LINC01500	ENST00000663641.1	n.830-6420A>G		intron_variant	Intron 5 of 5
LINC01500	ENST00000665985.1	n.693-6420A>G		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs17095819; hg19: chr14-59643961;