chr19-33359935-A-G

Variant names:

• chr19-33359935-A-G
• rs10518275

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 0.155 in 152,212 control chromosomes in the GnomAD database, including 2,178 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 0.16 (2178 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 8 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 (AMR) allele frequency at 95% confidence interval = 0.249 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: 0.155 AC: 23638 AN: 152094 Hom.: 2170 Cov.: 33

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.155 AC: 23664 AN: 152212 Hom.: 2178 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74420

African (AFR) AF: 0.0841 AC: 3495 AN: 41534

American (AMR) AF: 0.255 AC: 3905 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3466

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.0557 AC: 269 AN: 4828

European-Finnish (FIN) AF: 0.184 AC: 1945 AN: 10586

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12945 AN: 68006

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.177 Hom.: 2078

Bravo AF: 0.160

Asia WGS AF: 0.0410 AC: 144 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.76
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10518275; hg19: chr19-33850841;