rs12338022

Variant names:

• chr9-86594001-A-G
• rs12338022
• ENST00000739587.1:n.166+22623A>G

Variant summary

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

The ENST00000739587.1(ENSG00000232211):​n.166+22623A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,030 control chromosomes in the GnomAD database, including 30,808 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 0.62 (30808 hom., cov: 32)
• Consequence: ENSG00000232211 ENST00000739587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 2 publications found

Genes affected

ENSG00000232211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739587.1. 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
	ENSG00000232211	ENST00000739587.1		n.166+22623A>G		intron	N/A
	ENSG00000232211	ENST00000739590.1		n.272+1104A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93607 AN: 151912 Hom.: 30764 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.616 AC: 93714 AN: 152030 Hom.: 30808 Cov.: 32 AF XY: 0.615 AC XY: 45687 AN XY: 74318

African (AFR) AF: 0.861 AC: 35707 AN: 41492

American (AMR) AF: 0.559 AC: 8534 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2108 AN: 5142

South Asian (SAS) AF: 0.582 AC: 2806 AN: 4822

European-Finnish (FIN) AF: 0.537 AC: 5672 AN: 10558

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35055 AN: 67958

Other (OTH) AF: 0.606 AC: 1279 AN: 2112

Alfa AF: 0.570 Hom.: 7085

Bravo AF: 0.626

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.41

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: rs12338022;

hg19: chr9-89208916;