chr19-51091925-G-A

Variant names:

• chr19-51091925-G-A
• rs2691269

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 0.158 in 151,860 control chromosomes in the GnomAD database, including 2,063 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 0.16 (2063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 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: 0.158 AC: 23969 AN: 151742 Hom.: 2058 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.158 AC: 23990 AN: 151860 Hom.: 2063 Cov.: 32 AF XY: 0.159 AC XY: 11810 AN XY: 74190

African (AFR) AF: 0.190 AC: 7879 AN: 41414

American (AMR) AF: 0.0856 AC: 1307 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1076 AN: 5122

South Asian (SAS) AF: 0.148 AC: 714 AN: 4814

European-Finnish (FIN) AF: 0.238 AC: 2506 AN: 10542

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9451 AN: 67930

Other (OTH) AF: 0.137 AC: 288 AN: 2102

Alfa AF: 0.135 Hom.: 2256

Bravo AF: 0.146

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.90
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2691269; hg19: chr19-51595182;