rs9332467

Variant names:

• chr4-98874173-G-A
• rs9332467

Your query was ambiguous. Multiple possible variants found:

• chr4-98874173-G-A
• chr4-98874173-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.455 in 151,918 control chromosomes in the GnomAD database, including 17,061 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 0.45 (17061 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68959 AN: 151804 Hom.: 17027 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.461

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.455 AC: 69058 AN: 151918 Hom.: 17061 Cov.: 32 AF XY: 0.446 AC XY: 33112 AN XY: 74228

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.460

Alfa AF: 0.339 Hom.: 1588

Bravo AF: 0.469

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332467; hg19: chr4-99795324;