chr19-50383830-C-T

Variant names:

• chr19-50383830-C-T
• rs3219281

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 0.111 in 152,216 control chromosomes in the GnomAD database, including 1,074 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 0.11 (1074 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 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: 0.112 AC: 16967 AN: 152098 Hom.: 1076 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.111 AC: 16968 AN: 152216 Hom.: 1074 Cov.: 33 AF XY: 0.110 AC XY: 8188 AN XY: 74440

African (AFR) AF: 0.155 AC: 6440 AN: 41498

American (AMR) AF: 0.0996 AC: 1525 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.154 AC: 795 AN: 5174

South Asian (SAS) AF: 0.203 AC: 979 AN: 4826

European-Finnish (FIN) AF: 0.0401 AC: 426 AN: 10612

Middle Eastern (MID) AF: 0.131 AC: 38 AN: 290

European-Non Finnish (NFE) AF: 0.0848 AC: 5769 AN: 68018

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.102 Hom.: 1998

Bravo AF: 0.117

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		-0.62
PromoterAI		-0.033	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3219281; hg19: chr19-50887087;