19-10289228-C-T

Variant names:

• chr19-10289228-C-T
• rs2569693
• ENST00000724881.1:n.99G>A

Variant summary

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

The ENST00000724881.1(ICAM4-AS1):​n.99G>A 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 0.314 in 151,908 control chromosomes in the GnomAD database, including 9,109 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 0.31 (9109 hom., cov: 31)
• Consequence: ICAM4-AS1 ENST00000724881.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 22 publications found

Genes affected

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

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

ENSG00000294674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM4-AS1	NR_186335.1	n.-209G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM4-AS1	ENST00000724881.1	n.99G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LIMASI	ENST00000715961.1	n.395+1191G>A		intron_variant	Intron 1 of 2
ICAM4-AS1	ENST00000589379.1	n.-209G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47705 AN: 151790 Hom.: 9112 Cov.: 31

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.314 AC: 47693 AN: 151908 Hom.: 9109 Cov.: 31 AF XY: 0.316 AC XY: 23474 AN XY: 74212

African (AFR) AF: 0.0943 AC: 3913 AN: 41474

American (AMR) AF: 0.461 AC: 7046 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3464

East Asian (EAS) AF: 0.251 AC: 1291 AN: 5136

South Asian (SAS) AF: 0.455 AC: 2188 AN: 4810

European-Finnish (FIN) AF: 0.358 AC: 3780 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26735 AN: 67900

Other (OTH) AF: 0.360 AC: 757 AN: 2104

Alfa AF: 0.379 Hom.: 18805

Bravo AF: 0.313

Asia WGS AF: 0.351 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.8
DANN	Benign	0.89
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2569693; hg19: chr19-10399904;