rs9409929

Variant names:

• chr9-134448667-G-A
• rs9409929
• ENST00000745249.1:n.211+3347G>A

Variant summary

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

The ENST00000745249.1(ENSG00000228877):​n.211+3347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,100 control chromosomes in the GnomAD database, including 7,049 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 0.29 (7049 hom., cov: 33)
• Consequence: ENSG00000228877 ENST00000745249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 17 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745249.1. 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
	ENSG00000228877	ENST00000745249.1		n.211+3347G>A		intron	N/A
	ENSG00000228877	ENST00000745250.1		n.194+3347G>A		intron	N/A
	ENSG00000228877	ENST00000745251.1		n.119+3347G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44717 AN: 151982 Hom.: 7041 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.294 AC: 44748 AN: 152100 Hom.: 7049 Cov.: 33 AF XY: 0.293 AC XY: 21817 AN XY: 74352

African (AFR) AF: 0.190 AC: 7893 AN: 41510

American (AMR) AF: 0.284 AC: 4348 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5172

South Asian (SAS) AF: 0.342 AC: 1643 AN: 4810

European-Finnish (FIN) AF: 0.316 AC: 3343 AN: 10586

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24366 AN: 67958

Other (OTH) AF: 0.310 AC: 654 AN: 2110

Alfa AF: 0.329 Hom.: 21618

Bravo AF: 0.280

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		0.84

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: rs9409929;

hg19: chr9-137340513;