rs1267037

Positions:

• chr2-161241644-A-C
• chr2-161241644-A-G
• chr2-161241644-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110593.1(PSMD14-DT):​n.348+6880T>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.701 in 152,078 control chromosomes in the GnomAD database, including 39,019 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 0.70 (39019 hom., cov: 32)
• Consequence: PSMD14-DT NR_110593.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.44

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSMD14-DT	NR_110593.1	n.348+6880T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMD14-DT	ENST00000421122.7	n.380+6880T>G		intron_variant, non_coding_transcript_variant		3
PSMD14-DT	ENST00000445372.5	n.229+6880T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106628 AN: 151960 Hom.: 39021 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.701 AC: 106655 AN: 152078 Hom.: 39019 Cov.: 32 AF XY: 0.703 AC XY: 52252 AN XY: 74366

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.708

Alfa AF: 0.687 Hom.: 5427

Bravo AF: 0.700

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	22
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1267037; hg19: chr2-162098155;