3-23143671-G-C

Variant names:

• chr3-23143671-G-C
• rs13317243

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 0.147 in 152,128 control chromosomes in the GnomAD database, including 2,078 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 0.15 (2078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22419 AN: 152010 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.147 AC: 22431 AN: 152128 Hom.: 2078 Cov.: 32 AF XY: 0.147 AC XY: 10941 AN XY: 74356

African (AFR) AF: 0.0403 AC: 1672 AN: 41520

American (AMR) AF: 0.167 AC: 2543 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3470

East Asian (EAS) AF: 0.145 AC: 750 AN: 5178

South Asian (SAS) AF: 0.0761 AC: 367 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10568

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13913 AN: 67988

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.173 Hom.: 340

Bravo AF: 0.145

Asia WGS AF: 0.124 AC: 433 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	0.33
DANN	Benign	0.44
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs13317243; hg19: chr3-23185162;