rs3093030

chr19-10286727-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589379.1(ICAM4-AS1):n.2293G>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 0.383 in 363,998 control chromosomes in the GnomAD database, including 29,481 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 0.34 (10809 hom., cov: 31)
  • Exomes 𝑓: 0.41 (18672 hom.)
• Consequence: ICAM4-AS1 ENST00000589379.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ICAM4-AS1	ENST00000589379.1	n.2293G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52273 AN: 151886 Hom.: 10811 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.412 AC: 87290 AN: 211994 Hom.: 18672 Cov.: 2 AF XY: 0.416 AC XY: 44624 AN XY: 107258

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.524

Gnomad4 ASJ exome AF: 0.448

Gnomad4 EAS exome AF: 0.304

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.432

Gnomad4 OTH exome AF: 0.406

GnomAD4 genome AF: 0.344 AC: 52267 AN: 152004 Hom.: 10809 Cov.: 31 AF XY: 0.347 AC XY: 25751 AN XY: 74280

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.398

Alfa AF: 0.423 Hom.: 30373

Bravo AF: 0.342

Asia WGS AF: 0.355 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093030; hg19: chr19-10397403;