chr19-54295903-C-T

Position:

• chr19-54295903-C-T

Variant summary

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

The variant allele was found at a frequency of 0.0403 in 331,318 control chromosomes in the GnomAD database, including 806 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 0.061 (607 hom., cov: 32)
  • Exomes 𝑓: 0.023 (199 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9211 AN: 152008 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00969

Gnomad OTH AF: 0.0642

GnomAD4 exome AF: 0.0230 AC: 4129 AN: 179192 Hom.: 199 Cov.: 4 AF XY: 0.0220 AC XY: 2172 AN XY: 98578

Gnomad4 AFR exome AF: 0.0968

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.00753

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.0107

Gnomad4 FIN exome AF: 0.0257

Gnomad4 NFE exome AF: 0.00896

Gnomad4 OTH exome AF: 0.0289

GnomAD4 genome AF: 0.0607 AC: 9236 AN: 152126 Hom.: 607 Cov.: 32 AF XY: 0.0625 AC XY: 4650 AN XY: 74384

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.00971

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0381 Hom.: 138

Bravo AF: 0.0729

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10412494; hg19: chr19-54799755;