2-24397014-A-G

Variant names:

• chr2-24397014-A-G
• rs12470303
• ENST00000826690.1:n.130-7748A>G

Variant summary

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

The ENST00000826690.1(ENSG00000286829):​n.130-7748A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,114 control chromosomes in the GnomAD database, including 26,487 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 0.58 (26487 hom., cov: 33)
• Consequence: ENSG00000286829 ENST00000826690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 5 publications found

Genes affected

ENSG00000286829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000286829	ENST00000826690.1	n.130-7748A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87571 AN: 151996 Hom.: 26487 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.576 AC: 87583 AN: 152114 Hom.: 26487 Cov.: 33 AF XY: 0.583 AC XY: 43337 AN XY: 74366

African (AFR) AF: 0.384 AC: 15911 AN: 41480

American (AMR) AF: 0.701 AC: 10706 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2150 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3859 AN: 5182

South Asian (SAS) AF: 0.646 AC: 3115 AN: 4822

European-Finnish (FIN) AF: 0.686 AC: 7259 AN: 10588

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42484 AN: 67984

Other (OTH) AF: 0.600 AC: 1270 AN: 2116

Alfa AF: 0.612 Hom.: 48531

Bravo AF: 0.566

Asia WGS AF: 0.687 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.80
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs12470303; hg19: chr2-24619883;