19-33562965-C-T

Variant names:

• chr19-33562965-C-T
• rs12972735

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 0.429 in 152,042 control chromosomes in the GnomAD database, including 14,188 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 0.43 (14188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65201 AN: 151922 Hom.: 14169 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.429 AC: 65266 AN: 152042 Hom.: 14188 Cov.: 32 AF XY: 0.432 AC XY: 32150 AN XY: 74350

African (AFR) AF: 0.504 AC: 20897 AN: 41470

American (AMR) AF: 0.454 AC: 6940 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5148

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4814

European-Finnish (FIN) AF: 0.436 AC: 4611 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25867 AN: 67966

Other (OTH) AF: 0.437 AC: 923 AN: 2114

Alfa AF: 0.392 Hom.: 16076

Bravo AF: 0.436

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12972735; hg19: chr19-34053871;