ENST00000668450.1:n.587+1606A>G

Variant names:

• chr2-64839177-A-G
• rs741477
• ENST00000668450.1:n.587+1606A>G

Variant summary

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

The ENST00000668450.1(ENSG00000287123):​n.587+1606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,266 control chromosomes in the GnomAD database, including 720 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 0.084 (720 hom., cov: 31)
• Consequence: ENSG00000287123 ENST00000668450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

ENSG00000287123 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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
ENSG00000287123	ENST00000668450.1	n.587+1606A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12828 AN: 152148 Hom.: 716 Cov.: 31

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0843 AC: 12839 AN: 152266 Hom.: 720 Cov.: 31 AF XY: 0.0820 AC XY: 6102 AN XY: 74458

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.0544

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.110 Hom.: 1336

Bravo AF: 0.0782

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs741477; hg19: chr2-65066311;