12-91929924-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305639	ENST00000812104.1		n.180+6823G>A		intron	N/A

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 v4.9

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;