3-122294618-C-T

Variant names:

• chr3-122294618-C-T
• rs73186030

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 0.11 in 152,148 control chromosomes in the GnomAD database, including 1,206 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 0.11 (1206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16679 AN: 152030 Hom.: 1205 Cov.: 32

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.110 AC: 16676 AN: 152148 Hom.: 1206 Cov.: 32 AF XY: 0.111 AC XY: 8247 AN XY: 74376

African (AFR) AF: 0.0352 AC: 1461 AN: 41516

American (AMR) AF: 0.122 AC: 1865 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5184

South Asian (SAS) AF: 0.175 AC: 843 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1449 AN: 10564

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9502 AN: 67988

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.121 Hom.: 166

Bravo AF: 0.104

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs73186030; hg19: chr3-122013465;