rs6478109

Variant names:

• chr9-114806486-A-G
• rs6478109

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 0.74 in 152,026 control chromosomes in the GnomAD database, including 42,526 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 0.74 (42526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 82 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.740 AC: 112415 AN: 151908 Hom.: 42470 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.740 AC: 112533 AN: 152026 Hom.: 42526 Cov.: 31 AF XY: 0.739 AC XY: 54953 AN XY: 74316

African (AFR) AF: 0.889 AC: 36867 AN: 41492

American (AMR) AF: 0.742 AC: 11338 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2626 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2618 AN: 5156

South Asian (SAS) AF: 0.730 AC: 3514 AN: 4814

European-Finnish (FIN) AF: 0.698 AC: 7372 AN: 10558

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45912 AN: 67944

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.695 Hom.: 156463

Bravo AF: 0.747

Asia WGS AF: 0.668 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.9
DANN	Benign	0.68
PhyloP100		0.65
PromoterAI		-0.13	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6478109; hg19: chr9-117568766;