chr9-114754905-G-A

Variant names:

• chr9-114754905-G-A
• rs6478105

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 0.916 in 152,232 control chromosomes in the GnomAD database, including 64,094 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 0.92 (64094 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139387 AN: 152114 Hom.: 64037 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.916 AC: 139501 AN: 152232 Hom.: 64094 Cov.: 31 AF XY: 0.921 AC XY: 68526 AN XY: 74426

African (AFR) AF: 0.964 AC: 40028 AN: 41530

American (AMR) AF: 0.876 AC: 13398 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3240 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5164 AN: 5176

South Asian (SAS) AF: 0.977 AC: 4707 AN: 4818

European-Finnish (FIN) AF: 0.951 AC: 10088 AN: 10612

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59869 AN: 68012

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.920 Hom.: 36249

Bravo AF: 0.912

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6478105; hg19: chr9-117517185;