rs12489521

Variant names:

• chr3-30342573-A-G
• rs12489521
• ENST00000813769.1:n.506-1250T>C

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.506-1250T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 151,874 control chromosomes in the GnomAD database, including 55,426 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 0.85 (55426 hom., cov: 30)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227549	ENST00000813769.1	n.506-1250T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129167 AN: 151756 Hom.: 55369 Cov.: 30

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.851 AC: 129286 AN: 151874 Hom.: 55426 Cov.: 30 AF XY: 0.854 AC XY: 63362 AN XY: 74214

African (AFR) AF: 0.938 AC: 38910 AN: 41460

American (AMR) AF: 0.871 AC: 13248 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2628 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4671 AN: 5130

South Asian (SAS) AF: 0.893 AC: 4307 AN: 4822

European-Finnish (FIN) AF: 0.817 AC: 8645 AN: 10578

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.797 AC: 54143 AN: 67892

Other (OTH) AF: 0.828 AC: 1742 AN: 2104

Alfa AF: 0.807 Hom.: 99973

Bravo AF: 0.855

Asia WGS AF: 0.904 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.032
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12489521; hg19: chr3-30384065;