chr19-10288699-T-G

Position:

• chr19-10288699-T-G

Variant summary

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

The ENST00000589379.1(ICAM4-AS1):​n.321A>C 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 0.301 in 155,062 control chromosomes in the GnomAD database, including 7,530 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 0.30 (7364 hom., cov: 32)
  • Exomes 𝑓: 0.33 (166 hom.)
• Consequence: ICAM4-AS1 ENST00000589379.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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.321A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45611 AN: 151850 Hom.: 7347 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.328 AC: 1013 AN: 3092 Hom.: 166 Cov.: 0 AF XY: 0.327 AC XY: 591 AN XY: 1810

Gnomad4 AFR exome AF: 0.875

Gnomad4 AMR exome AF: 0.251

Gnomad4 ASJ exome AF: 0.350

Gnomad4 EAS exome AF: 0.0676

Gnomad4 SAS exome AF: 0.347

Gnomad4 FIN exome AF: 0.306

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.296

GnomAD4 genome AF: 0.301 AC: 45675 AN: 151970 Hom.: 7364 Cov.: 32 AF XY: 0.296 AC XY: 21955 AN XY: 74274

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.297

Alfa AF: 0.293 Hom.: 1506

Bravo AF: 0.301

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281438; hg19: chr19-10399375;