rs3820996

Positions:

• chr2-161244567-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110593.1(PSMD14-DT):​n.348+3957T>C variant causes a intron, non coding transcript 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 NR_110593.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMD14-DT	NR_110593.1	n.348+3957T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD14-DT	ENST00000421122.7	n.380+3957T>C		intron_variant, non_coding_transcript_variant		3
PSMD14-DT	ENST00000445372.5	n.229+3957T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.0681

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0785 Hom.: 361

Bravo AF: 0.139

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3820996; hg19: chr2-162101078;