ENST00000829679.1:n.276+4439C>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909357	XR_007095848.1	n.123+4542C>G		intron_variant	Intron 1 of 1
LOC124909357	XR_007095849.1	n.226+4439C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307904	ENST00000829679.1	n.276+4439C>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs11928013; hg19: chr3-25919933;