rs2358693

chr3-22532678-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.208

Alfa AF: 0.234 Hom.: 8631

Bravo AF: 0.228

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.5
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2358693; hg19: chr3-22574169;