9-22875746-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.765

Alfa AF: 0.813 Hom.: 22634

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4615664; hg19: chr9-22875745;