9-135135153-A-G

Variant names:

• chr9-135135153-A-G
• rs2031825
• ENST00000824619.1:n.1027-136A>G

Variant summary

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

The ENST00000824619.1(ENSG00000307225):​n.1027-136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,126 control chromosomes in the GnomAD database, including 41,824 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 0.74 (41824 hom., cov: 33)
• Consequence: ENSG00000307225 ENST00000824619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 3 publications found

Genes affected

ENSG00000307225 (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 (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824619.1. 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
	ENSG00000307225	ENST00000824619.1		n.1027-136A>G		intron	N/A
	ENSG00000307225	ENST00000824620.1		n.86-136A>G		intron	N/A
	ENSG00000307225	ENST00000824621.1		n.161-136A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111982 AN: 152008 Hom.: 41776 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.737 AC: 112077 AN: 152126 Hom.: 41824 Cov.: 33 AF XY: 0.732 AC XY: 54409 AN XY: 74342

African (AFR) AF: 0.845 AC: 35056 AN: 41490

American (AMR) AF: 0.641 AC: 9798 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2595 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2504 AN: 5172

South Asian (SAS) AF: 0.686 AC: 3302 AN: 4816

European-Finnish (FIN) AF: 0.710 AC: 7507 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48960 AN: 67994

Other (OTH) AF: 0.716 AC: 1513 AN: 2114

Alfa AF: 0.725 Hom.: 128394

Bravo AF: 0.736

Asia WGS AF: 0.646 AC: 2247 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	1.8
DANN	Benign	0.33
PhyloP100		-0.28

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: rs2031825;

hg19: chr9-138026999;