19-3928371-A-G

Variant names:

• chr19-3928371-A-G
• rs4807532

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 0.73 in 152,056 control chromosomes in the GnomAD database, including 41,928 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 0.73 (41928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.730 AC: 110872 AN: 151938 Hom.: 41873 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.730 AC: 110986 AN: 152056 Hom.: 41928 Cov.: 32 AF XY: 0.736 AC XY: 54664 AN XY: 74310

African (AFR) AF: 0.896 AC: 37186 AN: 41518

American (AMR) AF: 0.784 AC: 11959 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5065 AN: 5174

South Asian (SAS) AF: 0.793 AC: 3827 AN: 4826

European-Finnish (FIN) AF: 0.629 AC: 6640 AN: 10550

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41946 AN: 67952

Other (OTH) AF: 0.714 AC: 1507 AN: 2110

Alfa AF: 0.655 Hom.: 147364

Bravo AF: 0.746

Asia WGS AF: 0.890 AC: 3092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.82
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4807532; hg19: chr19-3928369;