rs2358693

Variant names:

• chr3-22532678-T-G
• rs2358693

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 0.227 in 152,074 control chromosomes in the GnomAD database, including 4,033 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 0.23 (4033 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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: 0.227 AC: 34486 AN: 151956 Hom.: 4024 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.227 AC: 34529 AN: 152074 Hom.: 4033 Cov.: 31 AF XY: 0.222 AC XY: 16522 AN XY: 74362

African (AFR) AF: 0.242 AC: 10018 AN: 41466

American (AMR) AF: 0.170 AC: 2600 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1242 AN: 5176

South Asian (SAS) AF: 0.126 AC: 608 AN: 4818

European-Finnish (FIN) AF: 0.214 AC: 2269 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16242 AN: 67972

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.236 Hom.: 18112

Bravo AF: 0.228

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.37
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs2358693; hg19: chr3-22574169;