chr19-39293512-G-A

Variant names:

• chr19-39293512-G-A
• rs8107861

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 0.139 in 152,006 control chromosomes in the GnomAD database, including 3,538 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 0.14 (3538 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.138 AC: 21024 AN: 151888 Hom.: 3531 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.139 AC: 21072 AN: 152006 Hom.: 3538 Cov.: 31 AF XY: 0.133 AC XY: 9915 AN XY: 74308

African (AFR) AF: 0.406 AC: 16815 AN: 41372

American (AMR) AF: 0.0621 AC: 948 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.0350 AC: 181 AN: 5176

South Asian (SAS) AF: 0.0507 AC: 244 AN: 4816

European-Finnish (FIN) AF: 0.0253 AC: 268 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0318 AC: 2161 AN: 67998

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0577 Hom.: 441

Bravo AF: 0.154

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.71
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs8107861; hg19: chr19-39784152;