19-52424786-C-A

Variant names:

• chr19-52424786-C-A
• rs9630874

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 0.15 in 152,160 control chromosomes in the GnomAD database, including 2,361 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 0.15 (2361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.149 AC: 22706 AN: 152042 Hom.: 2334 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.150 AC: 22789 AN: 152160 Hom.: 2361 Cov.: 32 AF XY: 0.152 AC XY: 11283 AN XY: 74408

African (AFR) AF: 0.296 AC: 12271 AN: 41472

American (AMR) AF: 0.117 AC: 1792 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.0838 AC: 434 AN: 5182

South Asian (SAS) AF: 0.102 AC: 492 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1476 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5343 AN: 68006

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.0984 Hom.: 1550

Bravo AF: 0.156

Asia WGS AF: 0.155 AC: 538 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	2.7
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9630874; hg19: chr19-52928039;