chr2-16458298-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000289364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000702490.1	n.308-5954G>A		intron_variant	Intron 3 of 3
ENSG00000289364	ENST00000702846.1	n.385-5954G>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

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.790

Alfa AF: 0.762 Hom.: 43975

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346751; hg19: chr2-16639566;