rs3820996

Variant names:

• chr2-161244567-A-G
• rs3820996
• ENST00000803730.1:n.183T>C

Variant summary

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

The ENST00000803730.1(PSMD14-DT):​n.183T>C 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 0.138 in 152,208 control chromosomes in the GnomAD database, including 2,658 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 0.14 (2658 hom., cov: 32)
• Consequence: PSMD14-DT ENST00000803730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 4 publications found

Genes affected

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

LINC01806 (HGNC:52599): (long intergenic non-protein coding RNA 1806)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803730.1. 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
	PSMD14-DT	NR_110593.1		n.348+3957T>C		intron	N/A
	LINC01806	NR_110163.1		n.-172A>G		upstream_gene	N/A
	LINC01806	NR_110164.1		n.-172A>G		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14-DT	ENST00000803730.1		n.183T>C		non_coding_transcript_exon	Exon 1 of 2
	LINC01806	ENST00000804019.1		n.24A>G		non_coding_transcript_exon	Exon 1 of 4
	PSMD14-DT	ENST00000421122.8	TSL:3	n.385+3957T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20878 AN: 152090 Hom.: 2633 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0681

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.138 AC: 20960 AN: 152208 Hom.: 2658 Cov.: 32 AF XY: 0.140 AC XY: 10442 AN XY: 74404

African (AFR) AF: 0.327 AC: 13562 AN: 41506

American (AMR) AF: 0.0715 AC: 1094 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0681 AC: 236 AN: 3468

East Asian (EAS) AF: 0.180 AC: 930 AN: 5166

South Asian (SAS) AF: 0.0901 AC: 435 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10592

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2892 AN: 68024

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.0794 Hom.: 431

Bravo AF: 0.139

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.54
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs3820996; hg19: chr2-162101078;