rs12351590

Variant names:

• chr9-12108916-G-A
• rs12351590
• ENST00000452685.1:n.205+7905C>T

Variant summary

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

The ENST00000452685.1(ENSG00000224935):​n.205+7905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,036 control chromosomes in the GnomAD database, including 59,345 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 0.88 (59345 hom., cov: 32)
• Consequence: ENSG00000224935 ENST00000452685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 5 publications found

Genes affected

ENSG00000224935 (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 (NFE) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375976	NR_188496.1	n.316+7905C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224935	ENST00000452685.1	n.205+7905C>T		intron_variant	Intron 3 of 3	3
ENSG00000224935	ENST00000663621.2	n.293+7905C>T		intron_variant	Intron 3 of 3
ENSG00000224935	ENST00000749186.1	n.233+7905C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133361 AN: 151918 Hom.: 59319 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.878 AC: 133431 AN: 152036 Hom.: 59345 Cov.: 32 AF XY: 0.871 AC XY: 64766 AN XY: 74326

African (AFR) AF: 0.848 AC: 35190 AN: 41480

American (AMR) AF: 0.766 AC: 11700 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3285 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2730 AN: 5128

South Asian (SAS) AF: 0.799 AC: 3855 AN: 4822

European-Finnish (FIN) AF: 0.933 AC: 9905 AN: 10612

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63783 AN: 67944

Other (OTH) AF: 0.872 AC: 1840 AN: 2110

Alfa AF: 0.924 Hom.: 88648

Bravo AF: 0.861

Asia WGS AF: 0.617 AC: 2151 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	0.81
DANN	Benign	0.28
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs12351590; hg19: chr9-12108916;