rs12424367

Variant names:

• chr12-91929924-G-A
• rs12424367
• ENST00000812104.1:n.180+6823G>A

Variant summary

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

The ENST00000812104.1(ENSG00000305639):​n.180+6823G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,868 control chromosomes in the GnomAD database, including 16,009 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 0.44 (16009 hom., cov: 31)
• Consequence: ENSG00000305639 ENST00000812104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 2 publications found

Genes affected

ENSG00000305639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369901	XR_007063580.1	n.842-573C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305639	ENST00000812104.1	n.180+6823G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66514 AN: 151750 Hom.: 15974 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.439 AC: 66602 AN: 151868 Hom.: 16009 Cov.: 31 AF XY: 0.436 AC XY: 32331 AN XY: 74196

African (AFR) AF: 0.639 AC: 26438 AN: 41404

American (AMR) AF: 0.429 AC: 6545 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3472

East Asian (EAS) AF: 0.107 AC: 551 AN: 5152

South Asian (SAS) AF: 0.481 AC: 2318 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3723 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24581 AN: 67912

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.394 Hom.: 4822

Bravo AF: 0.447

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.27
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12424367; hg19: chr12-92323700;