chr19-21592569-C-T

Position:

• chr19-21592569-C-T

Variant summary

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

The ENST00000594927.1(ENSG00000268240):​n.1438G>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 0.323 in 152,086 control chromosomes in the GnomAD database, including 8,171 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 0.32 (8168 hom., cov: 32)
  • Exomes 𝑓: 0.32 (3 hom.)
• Consequence: ENST00000594927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372323	XR_001754056.2	n.523-3779C>T		intron_variant, non_coding_transcript_variant
LOC101929007	XR_007067176.1	n.486+1114G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000594927.1	n.1438G>A		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49156 AN: 151896 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.319 AC: 23 AN: 72 Hom.: 3 Cov.: 0 AF XY: 0.310 AC XY: 18 AN XY: 58

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.386

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.323 AC: 49174 AN: 152014 Hom.: 8168 Cov.: 32 AF XY: 0.326 AC XY: 24198 AN XY: 74286

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.340

Alfa AF: 0.342 Hom.: 18155

Bravo AF: 0.323

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8112960; hg19: chr19-21775371;