19-55581433-C-T

Variant names:

• chr19-55581433-C-T
• rs1079082

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 0.184 in 152,158 control chromosomes in the GnomAD database, including 2,591 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 0.18 (2591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27977 AN: 152038 Hom.: 2595 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 27981 AN: 152158 Hom.: 2591 Cov.: 32 AF XY: 0.177 AC XY: 13188 AN XY: 74384

African (AFR) AF: 0.187 AC: 7771 AN: 41488

American (AMR) AF: 0.201 AC: 3081 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3472

East Asian (EAS) AF: 0.167 AC: 864 AN: 5180

South Asian (SAS) AF: 0.165 AC: 795 AN: 4828

European-Finnish (FIN) AF: 0.0989 AC: 1048 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13256 AN: 67986

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.166 Hom.: 929

Bravo AF: 0.192

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.66
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1079082; hg19: chr19-56092799;