rs2000467

Variant names:

• chr22-23899346-A-G
• rs2000467
• ENST00000703580.1:n.387-3236T>C

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.387-3236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,088 control chromosomes in the GnomAD database, including 34,441 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 0.67 (34441 hom., cov: 33)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 23 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703580.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290199	ENST00000703580.1		n.387-3236T>C		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.213-7880T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101968 AN: 151970 Hom.: 34385 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.671 AC: 102078 AN: 152088 Hom.: 34441 Cov.: 33 AF XY: 0.676 AC XY: 50232 AN XY: 74346

African (AFR) AF: 0.720 AC: 29888 AN: 41484

American (AMR) AF: 0.649 AC: 9925 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3468

East Asian (EAS) AF: 0.506 AC: 2617 AN: 5172

South Asian (SAS) AF: 0.758 AC: 3657 AN: 4824

European-Finnish (FIN) AF: 0.664 AC: 7017 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44353 AN: 67980

Other (OTH) AF: 0.660 AC: 1392 AN: 2108

Alfa AF: 0.661 Hom.: 47291

Bravo AF: 0.669

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.78
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs2000467; hg19: chr22-24241533;