rs9450902

Positions:

• chr6-88170505-C-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 0.157 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;