chr19-15716921-G-A

Variant names:

• chr19-15716921-G-A
• rs4312419

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 0.211 in 151,900 control chromosomes in the GnomAD database, including 3,128 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 0.21 (3128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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: 0.211 AC: 32039 AN: 151782 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.211 AC: 32070 AN: 151900 Hom.: 3128 Cov.: 31 AF XY: 0.209 AC XY: 15510 AN XY: 74262

African (AFR) AF: 0.222 AC: 9183 AN: 41328

American (AMR) AF: 0.152 AC: 2317 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.127 AC: 659 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1064 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2426 AN: 10574

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15101 AN: 67950

Other (OTH) AF: 0.180 AC: 380 AN: 2108

Alfa AF: 0.198 Hom.: 1559

Asia WGS AF: 0.164 AC: 570 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	1.8
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4312419; hg19: chr19-15827731;