19-51462741-C-T

Variant names:

• chr19-51462741-C-T
• rs36498

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;