3-145168923-T-C

Variant names:

• chr3-145168923-T-C
• rs12486562

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 0.302 in 151,878 control chromosomes in the GnomAD database, including 7,969 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 0.30 (7969 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.302 AC: 45803 AN: 151762 Hom.: 7962 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.302 AC: 45825 AN: 151878 Hom.: 7969 Cov.: 31 AF XY: 0.302 AC XY: 22375 AN XY: 74204

African (AFR) AF: 0.135 AC: 5589 AN: 41434

American (AMR) AF: 0.345 AC: 5270 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.182 AC: 939 AN: 5152

South Asian (SAS) AF: 0.244 AC: 1173 AN: 4798

European-Finnish (FIN) AF: 0.439 AC: 4627 AN: 10532

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25801 AN: 67926

Other (OTH) AF: 0.324 AC: 683 AN: 2108

Alfa AF: 0.332 Hom.: 3379

Bravo AF: 0.289

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.61
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12486562; hg19: chr3-144886710;