chr19-51449486-T-C

Position:

• chr19-51449486-T-C

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 0.386 in 152,090 control chromosomes in the GnomAD database, including 14,071 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 0.39 (14071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.385 AC: 58553 AN: 151972 Hom.: 14030 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.350

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.386 AC: 58644 AN: 152090 Hom.: 14071 Cov.: 32 AF XY: 0.386 AC XY: 28709 AN XY: 74362

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.352

Alfa AF: 0.288 Hom.: 2903

Bravo AF: 0.393

Asia WGS AF: 0.456 AC: 1589 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	2.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36485; hg19: chr19-51952740;