rs9450594

Variant names:

• chr6-86928621-G-T
• rs9450594

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 0.154 in 152,064 control chromosomes in the GnomAD database, including 2,406 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 0.15 (2406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.154 AC: 23339 AN: 151948 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.154 AC: 23405 AN: 152064 Hom.: 2406 Cov.: 32 AF XY: 0.151 AC XY: 11241 AN XY: 74334

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.146

Alfa AF: 0.113 Hom.: 1840

Bravo AF: 0.160

Asia WGS AF: 0.114 AC: 396 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9450594; hg19: chr6-87638339;