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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.454 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.661 AC: 27390 AN: 41420

American (AMR) AF: 0.402 AC: 6135 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1521 AN: 3468

East Asian (EAS) AF: 0.193 AC: 994 AN: 5162

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4812

European-Finnish (FIN) AF: 0.363 AC: 3817 AN: 10520

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26437 AN: 67948

Other (OTH) AF: 0.460 AC: 972 AN: 2112

Alfa AF: 0.349 Hom.: 1746

Bravo AF: 0.469

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.80
PhyloP100		-0.084
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9332467; hg19: chr4-99795324;