rs551120

Variant names:

• chr9-133014026-A-G
• rs551120

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 0.0395 in 152,212 control chromosomes in the GnomAD database, including 226 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 0.039 (226 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 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: 0.0395 AC: 6014 AN: 152096 Hom.: 227 Cov.: 33

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0395 AC: 6012 AN: 152212 Hom.: 226 Cov.: 33 AF XY: 0.0401 AC XY: 2982 AN XY: 74412

Gnomad4 AFR AF: 0.0740

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0276

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0370 Hom.: 57

Bravo AF: 0.0510

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs551120; hg19: chr9-135889413;