19-51462741-C-T

Variant names:

• chr19-51462741-C-T
• rs36498

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.451 AC: 18697 AN: 41448

American (AMR) AF: 0.164 AC: 2508 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2175 AN: 5150

South Asian (SAS) AF: 0.162 AC: 781 AN: 4820

European-Finnish (FIN) AF: 0.0894 AC: 949 AN: 10620

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7630 AN: 67990

Other (OTH) AF: 0.210 AC: 443 AN: 2110

Alfa AF: 0.153 Hom.: 8165

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
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs36498; hg19: chr19-51965995;