19-53788578-C-T

Variant summary

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

The ENST00000597420.2(ENSG00000269564):n.90-19C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 459,238 control chromosomes in the GnomAD database, including 5,998 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 0.15 (1849 hom., cov: 32)
  • Exomes 𝑓: 0.16 (4149 hom.)
• Consequence: ENST00000597420.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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
	ENST00000597420.2	n.90-19C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23088 AN: 151486 Hom.: 1851 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.158 AC: 48674 AN: 307666 Hom.: 4149 AF XY: 0.162 AC XY: 28238 AN XY: 174536

Gnomad4 AFR exome AF: 0.159

Gnomad4 AMR exome AF: 0.146

Gnomad4 ASJ exome AF: 0.119

Gnomad4 EAS exome AF: 0.0676

Gnomad4 SAS exome AF: 0.205

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.152 AC: 23095 AN: 151572 Hom.: 1849 Cov.: 32 AF XY: 0.154 AC XY: 11423 AN XY: 74006

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.126

Alfa AF: 0.137 Hom.: 1582

Bravo AF: 0.146

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12983273; hg19: chr19-54291832;