rs4465047

chr9-22872159-C-Achr9-22872159-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, non coding transcript 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: ENST00000640003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000640003.1	n.490+2039G>T		intron_variant, non_coding_transcript_variant		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;