3-25878442-C-G

Variant names:

• chr3-25878442-C-G
• rs11928013
• ENST00000829679.1:n.276+4439C>G

Variant summary

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

The ENST00000829679.1(ENSG00000307904):​n.276+4439C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,112 control chromosomes in the GnomAD database, including 3,125 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 0.12 (3125 hom., cov: 33)
• Consequence: ENSG00000307904 ENST00000829679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 1 publications found

Genes affected

ENSG00000307904 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307904	ENST00000829679.1		n.276+4439C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18088 AN: 151994 Hom.: 3111 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.119 AC: 18131 AN: 152112 Hom.: 3125 Cov.: 33 AF XY: 0.115 AC XY: 8584 AN XY: 74368

African (AFR) AF: 0.381 AC: 15809 AN: 41446

American (AMR) AF: 0.0605 AC: 925 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4820

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0136 AC: 925 AN: 67998

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0216 Hom.: 49

Bravo AF: 0.134

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.60
PhyloP100		0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11928013;

hg19: chr3-25919933;