ENST00000799111.1:n.91-14261A>G

Variant names:

• chr12-47574240-A-G
• rs739856
• ENST00000799111.1:n.91-14261A>G

Variant summary

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

The ENST00000799111.1(ENSG00000304045):​n.91-14261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,124 control chromosomes in the GnomAD database, including 9,488 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 0.32 (9488 hom., cov: 32)
• Consequence: ENSG00000304045 ENST00000799111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02
• Publications: 3 publications found

Genes affected

ENSG00000304045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799111.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304045	ENST00000799111.1		n.91-14261A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49013 AN: 152006 Hom.: 9487 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.322 AC: 49012 AN: 152124 Hom.: 9488 Cov.: 32 AF XY: 0.321 AC XY: 23887 AN XY: 74368

African (AFR) AF: 0.109 AC: 4508 AN: 41548

American (AMR) AF: 0.280 AC: 4282 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1692 AN: 5178

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4556 AN: 10548

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29847 AN: 67966

Other (OTH) AF: 0.332 AC: 701 AN: 2114

Alfa AF: 0.396 Hom.: 6498

Bravo AF: 0.301

Asia WGS AF: 0.294 AC: 1022 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.75
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs739856; hg19: chr12-47968023;