rs2227319

Variant names:

• chr17-40014592-G-A
• rs2227319
• ENST00000583462.1:n.38C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-40014592-G-A
• chr17-40014592-G-C

Variant summary

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

The ENST00000583462.1(PSMD3-AS1):​n.38C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,100 control chromosomes in the GnomAD database, including 8,405 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 0.31 (8400 hom., cov: 31)
  • Exomes 𝑓: 0.35 (5 hom.)
• Consequence: PSMD3-AS1 ENST00000583462.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 24 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583462.1. 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
	PSMD3-AS1	NR_198981.1		n.50C>T		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD3-AS1	ENST00000583462.1	TSL:3	n.38C>T		non_coding_transcript_exon	Exon 1 of 2
	PSMD3-AS1	ENST00000584649.1	TSL:4	n.114C>T		non_coding_transcript_exon	Exon 1 of 3
	PSMD3-AS1	ENST00000801108.1		n.127C>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46763 AN: 151870 Hom.: 8409 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.348 AC: 39 AN: 112 Hom.: 5 Cov.: 0 AF XY: 0.351 AC XY: 26 AN XY: 74

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.333 AC: 2 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.200 AC: 4 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.371 AC: 26 AN: 70

Other (OTH) AF: 0.429 AC: 6 AN: 14

GnomAD4 genome AF: 0.308 AC: 46751 AN: 151988 Hom.: 8400 Cov.: 31 AF XY: 0.309 AC XY: 22933 AN XY: 74272

African (AFR) AF: 0.115 AC: 4787 AN: 41498

American (AMR) AF: 0.399 AC: 6087 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2130 AN: 5134

South Asian (SAS) AF: 0.463 AC: 2230 AN: 4814

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25469 AN: 67928

Other (OTH) AF: 0.365 AC: 771 AN: 2112

Alfa AF: 0.312 Hom.: 5305

Bravo AF: 0.308

Asia WGS AF: 0.406 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2227319;

hg19: chr17-38170845;