chr18-55774818-T-G

Variant names:

• chr18-55774818-T-G
• rs2306163
• NR_145452.1:n.5984A>C

Variant summary

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

The NR_145452.1(LINC01415):​n.5984A>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 0.238 in 152,068 control chromosomes in the GnomAD database, including 5,351 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 0.24 (5351 hom., cov: 31)
• Consequence: LINC01415 NR_145452.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 2 publications found

Genes affected

LINC01415 (HGNC:50709): (long intergenic non-protein coding RNA 1415)

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01415	NR_145452.1	n.5984A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01415	NR_145453.1	n.5486A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01415	NR_145454.1	n.5276A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105372130	XR_007066382.1	n.329-10081T>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.519+2047T>G		intron_variant	Intron 4 of 4	4
ENSG00000267284	ENST00000589662.1	n.218-10081T>G		intron_variant	Intron 1 of 3	5
ENSG00000267284	ENST00000654829.1	n.157-10081T>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36124 AN: 151950 Hom.: 5348 Cov.: 31

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.238 AC: 36134 AN: 152068 Hom.: 5351 Cov.: 31 AF XY: 0.238 AC XY: 17660 AN XY: 74302

African (AFR) AF: 0.0626 AC: 2599 AN: 41512

American (AMR) AF: 0.368 AC: 5619 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3470

East Asian (EAS) AF: 0.145 AC: 746 AN: 5162

South Asian (SAS) AF: 0.174 AC: 838 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2879 AN: 10552

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21678 AN: 67974

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.196 Hom.: 580

Bravo AF: 0.237

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2306163; hg19: chr18-53442049;