12-48285832-T-C

Variant names:

• chr12-48285832-T-C
• rs1489111
• ENST00000717861.1:n.311+52165T>C

Variant summary

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

The ENST00000717861.1(ENSG00000293682):​n.311+52165T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,930 control chromosomes in the GnomAD database, including 40,100 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 0.72 (40100 hom., cov: 30)
• Consequence: ENSG00000293682 ENST00000717861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 7 publications found

Genes affected

ENSG00000293682 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369753	XR_944923.3	n.375-6381A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293682	ENST00000717861.1	n.311+52165T>C		intron_variant	Intron 3 of 4
ENSG00000303687	ENST00000796536.1	n.187-6381A>G		intron_variant	Intron 2 of 2
ENSG00000303687	ENST00000796537.1	n.382-6381A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109531 AN: 151812 Hom.: 40078 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.721 AC: 109601 AN: 151930 Hom.: 40100 Cov.: 30 AF XY: 0.714 AC XY: 53037 AN XY: 74260

African (AFR) AF: 0.715 AC: 29606 AN: 41402

American (AMR) AF: 0.604 AC: 9225 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2122 AN: 5144

South Asian (SAS) AF: 0.658 AC: 3164 AN: 4806

European-Finnish (FIN) AF: 0.716 AC: 7561 AN: 10564

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.775 AC: 52648 AN: 67964

Other (OTH) AF: 0.727 AC: 1532 AN: 2106

Alfa AF: 0.737 Hom.: 19151

Bravo AF: 0.712

Asia WGS AF: 0.543 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1489111; hg19: chr12-48679615;