chr9-31546474-A-G

Variant names:

• chr9-31546474-A-G
• rs4576506

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 0.915 in 152,198 control chromosomes in the GnomAD database, including 64,035 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 0.91 (64035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• 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 (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.915 AC: 139155 AN: 152080 Hom.: 64009 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.915 AC: 139234 AN: 152198 Hom.: 64035 Cov.: 32 AF XY: 0.918 AC XY: 68267 AN XY: 74404

African (AFR) AF: 0.815 AC: 33828 AN: 41488

American (AMR) AF: 0.923 AC: 14108 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3381 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5178

South Asian (SAS) AF: 0.981 AC: 4729 AN: 4820

European-Finnish (FIN) AF: 0.957 AC: 10158 AN: 10610

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64784 AN: 68026

Other (OTH) AF: 0.927 AC: 1956 AN: 2110

Alfa AF: 0.936 Hom.: 109043

Bravo AF: 0.908

Asia WGS AF: 0.970 AC: 3373 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	1.8
DANN	Benign	0.51
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs4576506; hg19: chr9-31546472;