19-10289628-G-A

Variant names:

• chr19-10289628-G-A
• rs281440
• ENST00000724727.1:n.448C>T

Variant summary

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

The ENST00000724727.1(ENSG00000294616):​n.448C>T 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 0.744 in 152,096 control chromosomes in the GnomAD database, including 42,444 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 0.74 (42444 hom., cov: 32)
• Consequence: ENSG00000294616 ENST00000724727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 25 publications found

Genes affected

ENSG00000294616 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294616	ENST00000724727.1		n.448C>T		non_coding_transcript_exon	Exon 2 of 2
	LIMASI	ENST00000715961.1		n.395+791C>T		intron	N/A
	ENSG00000294674	ENST00000725204.1		n.135+167G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113090 AN: 151978 Hom.: 42424 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.744 AC: 113157 AN: 152096 Hom.: 42444 Cov.: 32 AF XY: 0.743 AC XY: 55229 AN XY: 74340

African (AFR) AF: 0.707 AC: 29340 AN: 41516

American (AMR) AF: 0.766 AC: 11717 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2695 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2314 AN: 5140

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4820

European-Finnish (FIN) AF: 0.778 AC: 8238 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52635 AN: 67948

Other (OTH) AF: 0.771 AC: 1625 AN: 2108

Alfa AF: 0.765 Hom.: 138906

Bravo AF: 0.744

Asia WGS AF: 0.676 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.94
PhyloP100		-0.14
PromoterAI		0.092	Neutral

Splicing

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

Other links and lift over

dbSNP: rs281440; hg19: chr19-10400304; COSMIC: COSV53424152;