rs9493454

Variant names:

• chr6-132823490-A-C
• rs9493454

Your query was ambiguous. Multiple possible variants found:

• chr6-132823490-A-C
• chr6-132823490-A-T

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 0.202 in 149,796 control chromosomes in the GnomAD database, including 4,242 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 0.20 (4242 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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: 0.201 AC: 30143 AN: 149696 Hom.: 4228 Cov.: 30

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.202 AC: 30194 AN: 149796 Hom.: 4242 Cov.: 30 AF XY: 0.200 AC XY: 14618 AN XY: 72982

African (AFR) AF: 0.402 AC: 16357 AN: 40652

American (AMR) AF: 0.127 AC: 1893 AN: 14944

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 479 AN: 3454

East Asian (EAS) AF: 0.0807 AC: 412 AN: 5106

South Asian (SAS) AF: 0.181 AC: 862 AN: 4774

European-Finnish (FIN) AF: 0.160 AC: 1594 AN: 9956

Middle Eastern (MID) AF: 0.182 AC: 51 AN: 280

European-Non Finnish (NFE) AF: 0.118 AC: 8004 AN: 67640

Other (OTH) AF: 0.198 AC: 412 AN: 2086

Alfa AF: 0.110 Hom.: 270

Bravo AF: 0.205

Asia WGS AF: 0.184 AC: 642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.22
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9493454; hg19: chr6-133144629;