rs281439

Variant names:

• chr19-10289434-G-C
• rs281439
• ENST00000724727.1:n.642C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-10289434-G-C
• chr19-10289434-G-T

Variant summary

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

The ENST00000724727.1(ENSG00000294616):​n.642C>G 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 0.723 in 151,946 control chromosomes in the GnomAD database, including 40,203 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 0.72 (40203 hom., cov: 32)
• Consequence: ENSG00000294616 ENST00000724727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 24 publications found

Genes affected

ENSG00000294616 (HGNC:):

LIMASI (HGNC:56357): (lncRNA inflammatory and mucous response associated, antisense to ICAM1)

ICAM4-AS1 (HGNC:55990): (ICAM4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294616	ENST00000724727.1	n.642C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000294674	ENST00000725204.1	n.108G>C		non_coding_transcript_exon_variant	Exon 1 of 2
LIMASI	ENST00000715961.1	n.395+985C>G		intron_variant	Intron 1 of 2
ICAM4-AS1	ENST00000724881.1	n.-108C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109798 AN: 151830 Hom.: 40186 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.723 AC: 109861 AN: 151946 Hom.: 40203 Cov.: 32 AF XY: 0.723 AC XY: 53690 AN XY: 74268

African (AFR) AF: 0.632 AC: 26198 AN: 41450

American (AMR) AF: 0.760 AC: 11604 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2693 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2295 AN: 5092

South Asian (SAS) AF: 0.772 AC: 3713 AN: 4812

European-Finnish (FIN) AF: 0.780 AC: 8255 AN: 10584

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52623 AN: 67946

Other (OTH) AF: 0.758 AC: 1600 AN: 2110

Alfa AF: 0.659 Hom.: 1917

Bravo AF: 0.718

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.4
DANN	Benign	0.58
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs281439; hg19: chr19-10400110; COSMIC: COSV53424150;