rs2579103

Variant names:

• chr12-90239730-C-A
• rs2579103
• ENST00000722829.1:n.279-14126C>A

Variant summary

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

The ENST00000722829.1(ENSG00000294335):​n.279-14126C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,026 control chromosomes in the GnomAD database, including 47,071 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 0.78 (47071 hom., cov: 31)
• Consequence: ENSG00000294335 ENST00000722829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 6 publications found

Genes affected

ENSG00000294335 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294335	ENST00000722829.1	n.279-14126C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118863 AN: 151906 Hom.: 47006 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.783 AC: 118992 AN: 152026 Hom.: 47071 Cov.: 31 AF XY: 0.781 AC XY: 58011 AN XY: 74294

African (AFR) AF: 0.901 AC: 37363 AN: 41488

American (AMR) AF: 0.763 AC: 11662 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3472

East Asian (EAS) AF: 0.643 AC: 3316 AN: 5158

South Asian (SAS) AF: 0.789 AC: 3795 AN: 4808

European-Finnish (FIN) AF: 0.685 AC: 7230 AN: 10554

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50623 AN: 67960

Other (OTH) AF: 0.775 AC: 1634 AN: 2108

Alfa AF: 0.754 Hom.: 84500

Bravo AF: 0.790

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs2579103; hg19: chr12-90633507;