rs1409832

Variant names:

• chr9-134536579-T-G
• rs1409832
• ENST00000435284.3:n.990-8341T>G

Variant summary

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

The ENST00000435284.3(ENSG00000228877):​n.990-8341T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,962 control chromosomes in the GnomAD database, including 4,889 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 0.25 (4889 hom., cov: 30)
• Consequence: ENSG00000228877 ENST00000435284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 7 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435284.3. 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
	LOC100506532	NR_188441.1		n.184-8341T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228877	ENST00000435284.3	TSL:3	n.990-8341T>G		intron	N/A
	ENSG00000228877	ENST00000745249.1		n.1012-8341T>G		intron	N/A
	ENSG00000228877	ENST00000745250.1		n.271-8341T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37910 AN: 151844 Hom.: 4888 Cov.: 30

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.250 AC: 37925 AN: 151962 Hom.: 4889 Cov.: 30 AF XY: 0.251 AC XY: 18637 AN XY: 74266

African (AFR) AF: 0.215 AC: 8902 AN: 41460

American (AMR) AF: 0.263 AC: 4018 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 991 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5156

South Asian (SAS) AF: 0.424 AC: 2035 AN: 4794

European-Finnish (FIN) AF: 0.197 AC: 2077 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17143 AN: 67940

Other (OTH) AF: 0.281 AC: 593 AN: 2114

Alfa AF: 0.255 Hom.: 14213

Bravo AF: 0.248

Asia WGS AF: 0.373 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.49
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1409832;

hg19: chr9-137428425;