rs1346751

Variant names:

• chr2-16458298-C-T
• rs1346751
• ENST00000690331.2:n.427-5957G>A

Variant summary

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

The ENST00000690331.2(ENSG00000289364):​n.427-5957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 151,956 control chromosomes in the GnomAD database, including 47,997 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 0.79 (47997 hom., cov: 31)
• Consequence: ENSG00000289364 ENST00000690331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 6 publications found

Genes affected

ENSG00000289364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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
ENSG00000289364	ENST00000690331.2	n.427-5957G>A		intron_variant	Intron 2 of 2
ENSG00000289364	ENST00000702490.2	n.308-5954G>A		intron_variant	Intron 3 of 3
ENSG00000289364	ENST00000702846.2	n.439-5954G>A		intron_variant	Intron 2 of 2
ENSG00000289364	ENST00000766298.1	n.384+11595G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120108 AN: 151838 Hom.: 47951 Cov.: 31

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.791 AC: 120212 AN: 151956 Hom.: 47997 Cov.: 31 AF XY: 0.790 AC XY: 58615 AN XY: 74242

African (AFR) AF: 0.895 AC: 37162 AN: 41502

American (AMR) AF: 0.699 AC: 10667 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2680 AN: 3466

East Asian (EAS) AF: 0.926 AC: 4777 AN: 5160

South Asian (SAS) AF: 0.787 AC: 3782 AN: 4804

European-Finnish (FIN) AF: 0.736 AC: 7727 AN: 10496

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50893 AN: 67944

Other (OTH) AF: 0.790 AC: 1668 AN: 2112

Alfa AF: 0.763 Hom.: 53061

Bravo AF: 0.791

Asia WGS AF: 0.844 AC: 2931 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1346751; hg19: chr2-16639566;