rs9450902

Variant names:

• chr6-88170505-C-G
• rs9450902

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 0.157 in 152,044 control chromosomes in the GnomAD database, including 2,682 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 0.16 (2682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23820 AN: 151926 Hom.: 2677 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.157 AC: 23846 AN: 152044 Hom.: 2682 Cov.: 32 AF XY: 0.153 AC XY: 11373 AN XY: 74324

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.132

Alfa AF: 0.130 Hom.: 227

Bravo AF: 0.163

Asia WGS AF: 0.0680 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9450902; hg19: chr6-88880224;