19-54302487-C-T

Position:

• chr19-54302487-C-T

Variant summary

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

The ENST00000426257.1(ENSG00000234436):​n.287-612G>A 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 0.729 in 151,974 control chromosomes in the GnomAD database, including 41,710 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 0.73 (41700 hom., cov: 30)
  • Exomes 𝑓: 0.88 (10 hom.)
• Consequence: ENST00000426257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.863).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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
	ENST00000426257.1	n.287-612G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110650 AN: 151830 Hom.: 41658 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.885 AC: 23 AN: 26 Hom.: 10 Cov.: 0 AF XY: 0.850 AC XY: 17 AN XY: 20

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 0.850

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.729 AC: 110749 AN: 151948 Hom.: 41700 Cov.: 30 AF XY: 0.722 AC XY: 53588 AN XY: 74236

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.732

Alfa AF: 0.701 Hom.: 58679

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs651279; hg19: -;