12-33548231-T-C

Variant names:

• chr12-33548231-T-C
• rs9300212
• ENST00000779593.1:n.126-11614A>G

Variant summary

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

The ENST00000779593.1(ENSG00000301538):​n.126-11614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,020 control chromosomes in the GnomAD database, including 39,657 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 0.71 (39657 hom., cov: 31)
• Consequence: ENSG00000301538 ENST00000779593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 9 publications found

Genes affected

ENSG00000301538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779593.1. 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
	ENSG00000301538	ENST00000779593.1		n.126-11614A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107957 AN: 151902 Hom.: 39638 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.711 AC: 108017 AN: 152020 Hom.: 39657 Cov.: 31 AF XY: 0.705 AC XY: 52387 AN XY: 74286

African (AFR) AF: 0.593 AC: 24583 AN: 41424

American (AMR) AF: 0.619 AC: 9447 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2882 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1589 AN: 5158

South Asian (SAS) AF: 0.644 AC: 3101 AN: 4818

European-Finnish (FIN) AF: 0.840 AC: 8891 AN: 10586

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55078 AN: 67980

Other (OTH) AF: 0.716 AC: 1511 AN: 2110

Alfa AF: 0.756 Hom.: 87570

Bravo AF: 0.686

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.68
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9300212; hg19: chr12-33701166;