chr19-52422531-A-C

Variant names:

• chr19-52422531-A-C
• rs12608629

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 0.0657 in 152,340 control chromosomes in the GnomAD database, including 416 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 0.066 (416 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0658 AC: 10014 AN: 152222 Hom.: 416 Cov.: 34

Gnomad AFR AF: 0.0253

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0657 AC: 10016 AN: 152340 Hom.: 416 Cov.: 34 AF XY: 0.0660 AC XY: 4920 AN XY: 74500

African (AFR) AF: 0.0252 AC: 1048 AN: 41580

American (AMR) AF: 0.0859 AC: 1314 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.142 AC: 739 AN: 5188

South Asian (SAS) AF: 0.0745 AC: 360 AN: 4832

European-Finnish (FIN) AF: 0.0639 AC: 679 AN: 10620

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5378 AN: 68028

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0720 Hom.: 669

Bravo AF: 0.0660

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.7
DANN	Benign	0.44
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12608629; hg19: chr19-52925784;