chr19-22560056-G-A

Variant names:

• chr19-22560056-G-A
• rs9305000

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 0.172 in 151,976 control chromosomes in the GnomAD database, including 6,192 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 0.17 (6192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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: 0.172 AC: 26133 AN: 151858 Hom.: 6167 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.172 AC: 26210 AN: 151976 Hom.: 6192 Cov.: 32 AF XY: 0.169 AC XY: 12540 AN XY: 74302

African (AFR) AF: 0.535 AC: 22142 AN: 41376

American (AMR) AF: 0.0934 AC: 1426 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.103 AC: 529 AN: 5150

South Asian (SAS) AF: 0.0879 AC: 423 AN: 4812

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1042 AN: 67982

Other (OTH) AF: 0.124 AC: 262 AN: 2108

Alfa AF: 0.0620 Hom.: 6905

Bravo AF: 0.193

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.071
DANN	Benign	0.16
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9305000; hg19: chr19-22742858;