rs12518614

Variant names:

• chr5-6324180-A-G
• rs12518614
• ENST00000507444.1:n.144-11464T>C

Variant summary

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

The ENST00000507444.1(LINC02145):​n.144-11464T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,308 control chromosomes in the GnomAD database, including 183 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 0.042 (183 hom., cov: 33)
• Consequence: LINC02145 ENST00000507444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 5 publications found

Genes affected

LINC02145 (HGNC:53005): (long intergenic non-protein coding RNA 2145)

ENSG00000302884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02145	NR_028351.1	n.144-11464T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02145	ENST00000507444.1	n.144-11464T>C		intron_variant	Intron 1 of 1	1
ENSG00000302884	ENST00000790215.1	n.278-1283A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6352 AN: 152190 Hom.: 183 Cov.: 33

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0417 AC: 6350 AN: 152308 Hom.: 183 Cov.: 33 AF XY: 0.0408 AC XY: 3038 AN XY: 74486

African (AFR) AF: 0.0100 AC: 416 AN: 41594

American (AMR) AF: 0.0358 AC: 548 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0182 AC: 88 AN: 4826

European-Finnish (FIN) AF: 0.0642 AC: 681 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4440 AN: 68010

Other (OTH) AF: 0.0312 AC: 66 AN: 2116

Alfa AF: 0.0553 Hom.: 641

Bravo AF: 0.0375

Asia WGS AF: 0.00896 AC: 31 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.73
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs12518614; hg19: chr5-6324293;