rs551120

Variant names:

• chr9-133014026-A-G
• rs551120
• ENST00000812269.1:n.66-3418T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000812269.1(ENSG00000305661):​n.66-3418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000305661 ENST00000812269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 1 publications found

Genes affected

ENSG00000305661 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812269.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305661	ENST00000812269.1		n.66-3418T>C		intron	N/A

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

African (AFR) AF: 0.0740 AC: 3076 AN: 41558

American (AMR) AF: 0.119 AC: 1822 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0276 AC: 132 AN: 4780

European-Finnish (FIN) AF: 0.0143 AC: 152 AN: 10614

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0103 AC: 698 AN: 68002

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs551120; hg19: chr9-135889413;