chr3-22553341-C-T

Variant names:

• chr3-22553341-C-T
• rs17011585

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 0.125 in 152,028 control chromosomes in the GnomAD database, including 1,334 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 0.12 (1334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 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: 0.125 AC: 18920 AN: 151910 Hom.: 1332 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0629

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.125 AC: 18952 AN: 152028 Hom.: 1334 Cov.: 32 AF XY: 0.124 AC XY: 9236 AN XY: 74292

African (AFR) AF: 0.191 AC: 7890 AN: 41416

American (AMR) AF: 0.0628 AC: 960 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3472

East Asian (EAS) AF: 0.169 AC: 874 AN: 5172

South Asian (SAS) AF: 0.146 AC: 702 AN: 4812

European-Finnish (FIN) AF: 0.0978 AC: 1032 AN: 10550

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6889 AN: 67998

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.103 Hom.: 1517

Bravo AF: 0.123

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.60
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17011585; hg19: chr3-22594832;