chr19-50854664-G-A

Variant names:

• chr19-50854664-G-A
• rs4802754

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 0.229 in 151,760 control chromosomes in the GnomAD database, including 4,767 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 0.23 (4767 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.229 AC: 34750 AN: 151642 Hom.: 4761 Cov.: 30

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.229 AC: 34769 AN: 151760 Hom.: 4767 Cov.: 30 AF XY: 0.231 AC XY: 17157 AN XY: 74144

African (AFR) AF: 0.0885 AC: 3667 AN: 41418

American (AMR) AF: 0.327 AC: 4998 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3462

East Asian (EAS) AF: 0.353 AC: 1812 AN: 5136

South Asian (SAS) AF: 0.166 AC: 798 AN: 4800

European-Finnish (FIN) AF: 0.348 AC: 3649 AN: 10496

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18288 AN: 67866

Other (OTH) AF: 0.223 AC: 471 AN: 2108

Alfa AF: 0.263 Hom.: 2914

Bravo AF: 0.222

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.92
PhyloP100		-0.33
PromoterAI		-0.0098	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4802754; hg19: chr19-51357920;