19-33832309-T-C

Variant names:

• chr19-33832309-T-C
• rs415237

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 0.612 in 151,948 control chromosomes in the GnomAD database, including 28,864 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 0.61 (28864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 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: 0.612 AC: 92962 AN: 151830 Hom.: 28856 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.612 AC: 93014 AN: 151948 Hom.: 28864 Cov.: 31 AF XY: 0.612 AC XY: 45409 AN XY: 74244

African (AFR) AF: 0.589 AC: 24417 AN: 41428

American (AMR) AF: 0.632 AC: 9654 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1591 AN: 5144

South Asian (SAS) AF: 0.574 AC: 2757 AN: 4804

European-Finnish (FIN) AF: 0.644 AC: 6803 AN: 10556

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43676 AN: 67958

Other (OTH) AF: 0.605 AC: 1277 AN: 2110

Alfa AF: 0.631 Hom.: 3766

Bravo AF: 0.611

Asia WGS AF: 0.460 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs415237; hg19: chr19-34323214;