19-6552375-C-T

Variant names:

• chr19-6552375-C-T
• rs348384
• ENST00000594355.1:n.523G>A

Variant summary

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

The ENST00000594355.1(ENSG00000268742):​n.523G>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 0.217 in 152,864 control chromosomes in the GnomAD database, including 4,269 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 0.22 (4267 hom., cov: 32)
  • Exomes 𝑓: 0.087 (2 hom.)
• Consequence: ENSG00000268742 ENST00000594355.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

Genes affected

ENSG00000268742 (HGNC:56999):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268742	ENST00000594355.1	n.523G>A		non_coding_transcript_exon_variant	Exon 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33064 AN: 152060 Hom.: 4263 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.0875 AC: 60 AN: 686 Hom.: 2 Cov.: 0 AF XY: 0.0909 AC XY: 40 AN XY: 440

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0429

Gnomad4 FIN exome AF: 0.0577

Gnomad4 NFE exome AF: 0.0966

Gnomad4 OTH exome AF: 0.0882

GnomAD4 genome AF: 0.217 AC: 33068 AN: 152178 Hom.: 4267 Cov.: 32 AF XY: 0.211 AC XY: 15674 AN XY: 74394

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.213

Alfa AF: 0.266 Hom.: 7302

Bravo AF: 0.218

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348384; hg19: chr19-6552386;