3-193394076-C-T

Variant names:

• chr3-193394076-C-T
• rs902192

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 0.199 in 152,000 control chromosomes in the GnomAD database, including 3,108 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 0.20 (3108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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: 0.199 AC: 30195 AN: 151882 Hom.: 3100 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.199 AC: 30230 AN: 152000 Hom.: 3108 Cov.: 32 AF XY: 0.195 AC XY: 14497 AN XY: 74308

African (AFR) AF: 0.235 AC: 9733 AN: 41408

American (AMR) AF: 0.228 AC: 3485 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3472

East Asian (EAS) AF: 0.0938 AC: 485 AN: 5172

South Asian (SAS) AF: 0.139 AC: 670 AN: 4820

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10544

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13103 AN: 67984

Other (OTH) AF: 0.186 AC: 393 AN: 2112

Alfa AF: 0.192 Hom.: 12080

Bravo AF: 0.207

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.33
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs902192; hg19: chr3-193111865;