rs6478915

chr9-129762171-G-A

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 0.778 in 152,016 control chromosomes in the GnomAD database, including 46,308 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 0.78 (46308 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.778 AC: 118165 AN: 151898 Hom.: 46269 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.778 AC: 118260 AN: 152016 Hom.: 46308 Cov.: 30 AF XY: 0.780 AC XY: 57966 AN XY: 74296

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.773

Alfa AF: 0.761 Hom.: 8957

Bravo AF: 0.788

Asia WGS AF: 0.883 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.13
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6478915; hg19: chr9-132524450;