rs10425222

Positions:

• chr19-53788945-C-A

Variant summary

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

The ENST00000597420.2(ENSG00000269564):​n.438C>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 0.0687 in 299,482 control chromosomes in the GnomAD database, including 1,281 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 0.083 (847 hom., cov: 32)
  • Exomes 𝑓: 0.054 (434 hom.)
• Consequence: ENSG00000269564 ENST00000597420.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

Genes affected

ENSG00000269564 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53788945C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000269564	ENST00000597420.2	n.438C>A		non_coding_transcript_exon_variant	2/2	6

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12567 AN: 151802 Hom.: 847 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0772

GnomAD4 exome AF: 0.0541 AC: 7989 AN: 147562 Hom.: 434 Cov.: 0 AF XY: 0.0608 AC XY: 4969 AN XY: 81704

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.0434

Gnomad4 ASJ exome AF: 0.0217

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0147

Gnomad4 NFE exome AF: 0.0339

Gnomad4 OTH exome AF: 0.0495

GnomAD4 genome AF: 0.0828 AC: 12576 AN: 151920 Hom.: 847 Cov.: 32 AF XY: 0.0822 AC XY: 6102 AN XY: 74268

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0797

Alfa AF: 0.0513 Hom.: 60

Bravo AF: 0.0897

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
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: rs10425222; hg19: chr19-54292199;