rs495828

Variant names:

• chr9-133279294-T-G
• rs495828

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 0.809 in 152,092 control chromosomes in the GnomAD database, including 50,070 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 0.81 (50070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.809 AC: 122993 AN: 151974 Hom.: 50005 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.809 AC: 123116 AN: 152092 Hom.: 50070 Cov.: 31 AF XY: 0.812 AC XY: 60402 AN XY: 74350

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.805

Alfa AF: 0.808 Hom.: 5507

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs495828; hg19: chr9-136154867;