9-22872159-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640003.1. 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
	ENSG00000284418	ENST00000640003.1	TSL:5	n.490+2039G>T		intron	N/A
	ENSG00000284418	ENST00000764217.1		n.240+2039G>T		intron	N/A
	ENSG00000284418	ENST00000764218.1		n.240+2039G>T		intron	N/A

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

African (AFR) AF: 0.681 AC: 28182 AN: 41386

American (AMR) AF: 0.811 AC: 12376 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2523 AN: 5150

South Asian (SAS) AF: 0.713 AC: 3412 AN: 4786

European-Finnish (FIN) AF: 0.869 AC: 9183 AN: 10570

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58622 AN: 67970

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.840 Hom.: 31687

Bravo AF: 0.783

Asia WGS AF: 0.620 AC: 2159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4465047; hg19: chr9-22872158;