ENST00000669568.1:n.296+12814A>G

Variant names:

• chr6-21258023-T-C
• rs2876587
• ENST00000669568.1:n.296+12814A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669568.1(ENSG00000287404):​n.296+12814A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,068 control chromosomes in the GnomAD database, including 50,036 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 0.81 (50036 hom., cov: 31)
• Consequence: ENSG00000287404 ENST00000669568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

ENSG00000287404 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 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
ENSG00000287404	ENST00000669568.1	n.296+12814A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122530 AN: 151950 Hom.: 49996 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.806 AC: 122627 AN: 152068 Hom.: 50036 Cov.: 31 AF XY: 0.804 AC XY: 59798 AN XY: 74374

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.823

Alfa AF: 0.846 Hom.: 12552

Bravo AF: 0.794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876587; hg19: chr6-21258254;