ENST00000658889.1:n.3153+5279A>G

Variant names:

• chr2-206887170-A-G
• rs1530941
• ENST00000658889.1:n.3153+5279A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000658889.1(ENSG00000229321):​n.3153+5279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,096 control chromosomes in the GnomAD database, including 7,732 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 0.31 (7732 hom., cov: 32)
• Consequence: ENSG00000229321 ENST00000658889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 2 publications found

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658889.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229321	ENST00000658889.1		n.3153+5279A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46922 AN: 151978 Hom.: 7733 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.309 AC: 46939 AN: 152096 Hom.: 7732 Cov.: 32 AF XY: 0.305 AC XY: 22689 AN XY: 74346

African (AFR) AF: 0.198 AC: 8214 AN: 41520

American (AMR) AF: 0.294 AC: 4486 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1638 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1043 AN: 4808

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10564

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25557 AN: 67986

Other (OTH) AF: 0.346 AC: 732 AN: 2116

Alfa AF: 0.349 Hom.: 4944

Bravo AF: 0.301

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.83
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1530941; hg19: chr2-207751894;