19-54295903-C-T

Variant names:

• chr19-54295903-C-T
• rs10412494

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;