rs6478105

chr9-114754905-G-Achr9-114754905-G-C

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 0.916 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.895

Alfa AF: 0.911 Hom.: 9338

Bravo AF: 0.912

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	11
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6478105; hg19: chr9-117517185;