3-42254314-A-G

Variant names:

• chr3-42254314-A-G
• rs9311317

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 0.303 in 152,010 control chromosomes in the GnomAD database, including 7,889 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 (7889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.303 AC: 45979 AN: 151892 Hom.: 7876 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.303 AC: 46032 AN: 152010 Hom.: 7889 Cov.: 32 AF XY: 0.307 AC XY: 22831 AN XY: 74282

African (AFR) AF: 0.347 AC: 14376 AN: 41456

American (AMR) AF: 0.274 AC: 4184 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4163 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1565 AN: 4806

European-Finnish (FIN) AF: 0.311 AC: 3279 AN: 10556

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16731 AN: 67966

Other (OTH) AF: 0.295 AC: 622 AN: 2108

Alfa AF: 0.268 Hom.: 25790

Bravo AF: 0.306

Asia WGS AF: 0.544 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9311317; hg19: chr3-42295806;