rs4465047

Variant names:

• chr9-22872159-C-A
• rs4465047
• ENST00000640003.1:n.490+2039G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-22872159-C-A
• chr9-22872159-C-T

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.490+2039G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 151,914 control chromosomes in the GnomAD database, including 48,201 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 0.79 (48201 hom., cov: 30)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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
ENSG00000284418	ENST00000640003.1	n.490+2039G>T		intron_variant	Intron 4 of 9	5

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119922 AN: 151796 Hom.: 48178 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.790 AC: 119997 AN: 151914 Hom.: 48201 Cov.: 30 AF XY: 0.788 AC XY: 58463 AN XY: 74238

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.789

Alfa AF: 0.841 Hom.: 28702

Bravo AF: 0.783

Asia WGS AF: 0.620 AC: 2159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4465047; hg19: chr9-22872158;