rs6478109

Positions:

• chr9-114806486-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.720

Alfa AF: 0.683 Hom.: 77351

Bravo AF: 0.747

Asia WGS AF: 0.668 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6478109; hg19: chr9-117568766;