rs17714461

Variant names:

• chr19-50921850-G-A
• rs17714461

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 0.0828 in 152,200 control chromosomes in the GnomAD database, including 676 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 0.083 (676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12606 AN: 152080 Hom.: 677 Cov.: 32

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0310

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0828 AC: 12604 AN: 152200 Hom.: 676 Cov.: 32 AF XY: 0.0816 AC XY: 6070 AN XY: 74412

African (AFR) AF: 0.0257 AC: 1068 AN: 41536

American (AMR) AF: 0.0881 AC: 1347 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0308 AC: 148 AN: 4808

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7975 AN: 68012

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.106 Hom.: 1900

Bravo AF: 0.0783

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs17714461; hg19: chr19-51425106;