rs2000467

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000290199	ENST00000703580.1	n.387-3236T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.660

Alfa AF: 0.658 Hom.: 32909

Bravo AF: 0.669

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
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: rs2000467; hg19: chr22-24241533;