12-98424524-C-T

Variant names:

• chr12-98424524-C-T
• rs1468832
• ENST00000789811.1:n.111-316G>A

Variant summary

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

The ENST00000789811.1(ENSG00000302820):​n.111-316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,194 control chromosomes in the GnomAD database, including 1,213 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 0.11 (1213 hom., cov: 32)
• Consequence: ENSG00000302820 ENST00000789811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 5 publications found

Genes affected

ENSG00000302820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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
ENSG00000302820	ENST00000789811.1	n.111-316G>A		intron_variant	Intron 1 of 2
ENSG00000302820	ENST00000789812.1	n.147-316G>A		intron_variant	Intron 1 of 4
ENSG00000302820	ENST00000789813.1	n.96+15173G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16173 AN: 152076 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.106 AC: 16188 AN: 152194 Hom.: 1213 Cov.: 32 AF XY: 0.104 AC XY: 7776 AN XY: 74430

African (AFR) AF: 0.218 AC: 9039 AN: 41478

American (AMR) AF: 0.0724 AC: 1108 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3468

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5186

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4830

European-Finnish (FIN) AF: 0.0790 AC: 837 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4191 AN: 68016

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0745 Hom.: 2440

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1468832; hg19: chr12-98818302;