rs2354225

Variant names:

• chr19-39557767-G-A
• rs2354225

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 0.182 in 152,174 control chromosomes in the GnomAD database, including 3,151 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 0.18 (3151 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27755 AN: 152056 Hom.: 3152 Cov.: 32

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.182 AC: 27748 AN: 152174 Hom.: 3151 Cov.: 32 AF XY: 0.193 AC XY: 14317 AN XY: 74366

African (AFR) AF: 0.0413 AC: 1717 AN: 41532

American (AMR) AF: 0.185 AC: 2832 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1238 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1503 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3252 AN: 10560

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15830 AN: 68008

Other (OTH) AF: 0.186 AC: 394 AN: 2114

Alfa AF: 0.203 Hom.: 594

Bravo AF: 0.166

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.87
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2354225; hg19: chr19-40048407;