chr19-51462741-C-T

Position:

• chr19-51462741-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 0.222 in 152,106 control chromosomes in the GnomAD database, including 5,607 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 0.22 (5607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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: 0.222 AC: 33741 AN: 151988 Hom.: 5585 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.222 AC: 33801 AN: 152106 Hom.: 5607 Cov.: 32 AF XY: 0.220 AC XY: 16348 AN XY: 74354

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0894

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.210

Alfa AF: 0.128 Hom.: 2141

Bravo AF: 0.239

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.026
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36498; hg19: chr19-51965995;