19-45305950-T-C

Variant names:

• chr19-45305950-T-C
• rs8111989

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 0.35 in 151,846 control chromosomes in the GnomAD database, including 10,056 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 0.35 (10056 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53100 AN: 151728 Hom.: 10039 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.350 AC: 53149 AN: 151846 Hom.: 10056 Cov.: 31 AF XY: 0.348 AC XY: 25856 AN XY: 74214

African (AFR) AF: 0.498 AC: 20584 AN: 41346

American (AMR) AF: 0.232 AC: 3530 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3470

East Asian (EAS) AF: 0.157 AC: 811 AN: 5170

South Asian (SAS) AF: 0.397 AC: 1909 AN: 4804

European-Finnish (FIN) AF: 0.329 AC: 3466 AN: 10550

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20729 AN: 67958

Other (OTH) AF: 0.327 AC: 687 AN: 2102

Alfa AF: 0.325 Hom.: 5157

Bravo AF: 0.345

Asia WGS AF: 0.292 AC: 1019 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs8111989; hg19: chr19-45809208;