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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376123	XR_930068.3	n.723-732A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232211	ENST00000739587.1	n.166+22623A>G		intron_variant	Intron 1 of 2
ENSG00000232211	ENST00000739590.1	n.272+1104A>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs12338022; hg19: chr9-89208916;