18-44475307-C-A

Variant names:

• chr18-44475307-C-A
• rs2359894
• ENST00000587877.2:n.396+42918G>T

Variant summary

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

The ENST00000587877.2(LINC01478):​n.396+42918G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,022 control chromosomes in the GnomAD database, including 6,487 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 0.29 (6487 hom., cov: 32)
• Consequence: LINC01478 ENST00000587877.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 3 publications found

Genes affected

LINC01478 (HGNC:51121): (long intergenic non-protein coding RNA 1478)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587877.2. 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
	LINC01478	NR_110792.1		n.386+42918G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01478	ENST00000587877.2	TSL:1	n.396+42918G>T		intron	N/A
	LINC01478	ENST00000591487.1	TSL:4	n.339+42918G>T		intron	N/A
	LINC01478	ENST00000653402.2		n.553+5612G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43490 AN: 151902 Hom.: 6475 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.286 AC: 43549 AN: 152022 Hom.: 6487 Cov.: 32 AF XY: 0.283 AC XY: 21055 AN XY: 74312

African (AFR) AF: 0.240 AC: 9954 AN: 41470

American (AMR) AF: 0.336 AC: 5129 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1936 AN: 5174

South Asian (SAS) AF: 0.218 AC: 1048 AN: 4804

European-Finnish (FIN) AF: 0.257 AC: 2716 AN: 10560

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20672 AN: 67968

Other (OTH) AF: 0.279 AC: 591 AN: 2116

Alfa AF: 0.297 Hom.: 18786

Bravo AF: 0.291

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.53
DANN	Benign	0.51
PhyloP100		-0.18

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: rs2359894;

hg19: chr18-42055272;