chr2-161250784-G-T

Position:

• chr2-161250784-G-T

Variant summary

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

The ENST00000421122.7(PSMD14-DT):​n.318+212C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,962 control chromosomes in the GnomAD database, including 29,486 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 0.61 (29486 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PSMD14-DT ENST00000421122.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

PSMD14-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMD14-DT	NR_110593.1	n.286+212C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD14-DT	ENST00000421122.7	n.318+212C>A		intron_variant		3
PSMD14-DT	ENST00000435692.6	n.666+212C>A		intron_variant		5
PSMD14-DT	ENST00000445372.5	n.167+212C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92816 AN: 151844 Hom.: 29487 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.611 AC: 92827 AN: 151962 Hom.: 29486 Cov.: 32 AF XY: 0.610 AC XY: 45281 AN XY: 74280

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.625

Alfa AF: 0.685 Hom.: 59270

Bravo AF: 0.615

Asia WGS AF: 0.519 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3731769; hg19: chr2-162107295;