9-22875746-C-T

Variant names:

• chr9-22875746-C-T
• rs4615664
• ENST00000640003.1:n.369-1427G>A

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.369-1427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,030 control chromosomes in the GnomAD database, including 44,666 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 0.76 (44666 hom., cov: 31)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 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.369-1427G>A		intron_variant	Intron 3 of 9	5
ENSG00000284418	ENST00000764217.1	n.119-1427G>A		intron_variant	Intron 1 of 5
ENSG00000284418	ENST00000764218.1	n.119-1427G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115291 AN: 151912 Hom.: 44651 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.759 AC: 115356 AN: 152030 Hom.: 44666 Cov.: 31 AF XY: 0.757 AC XY: 56265 AN XY: 74310

African (AFR) AF: 0.628 AC: 26012 AN: 41420

American (AMR) AF: 0.798 AC: 12191 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

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

South Asian (SAS) AF: 0.694 AC: 3350 AN: 4826

European-Finnish (FIN) AF: 0.841 AC: 8880 AN: 10556

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56765 AN: 68006

Other (OTH) AF: 0.765 AC: 1615 AN: 2112

Alfa AF: 0.811 Hom.: 25395

Bravo AF: 0.751

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs4615664; hg19: chr9-22875745;