17-40000459-C-T

Variant names:

• chr17-40000459-C-T
• rs4794822
• ENST00000801108.1:n.538-11564G>A

Variant summary

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

The ENST00000801108.1(PSMD3-AS1):​n.538-11564G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,990 control chromosomes in the GnomAD database, including 10,110 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 0.36 (10110 hom., cov: 32)
• Consequence: PSMD3-AS1 ENST00000801108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 50 publications found

Genes affected

PSMD3-AS1 (HGNC:58140):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801108.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD3-AS1	ENST00000801108.1		n.538-11564G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55063 AN: 151872 Hom.: 10096 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.363 AC: 55129 AN: 151990 Hom.: 10110 Cov.: 32 AF XY: 0.361 AC XY: 26821 AN XY: 74282

African (AFR) AF: 0.315 AC: 13078 AN: 41466

American (AMR) AF: 0.345 AC: 5269 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2384 AN: 5156

South Asian (SAS) AF: 0.254 AC: 1227 AN: 4826

European-Finnish (FIN) AF: 0.397 AC: 4191 AN: 10548

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26594 AN: 67960

Other (OTH) AF: 0.339 AC: 715 AN: 2108

Alfa AF: 0.377 Hom.: 30664

Bravo AF: 0.357

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4794822; hg19: chr17-38156712;