2-161257549-A-G

Variant names:

• chr2-161257549-A-G
• rs1882364
• ENST00000435692.6:n.344-2869T>C

Variant summary

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

The ENST00000435692.6(PSMD14-DT):​n.344-2869T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,026 control chromosomes in the GnomAD database, including 35,488 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 0.68 (35488 hom., cov: 32)
• Consequence: PSMD14-DT ENST00000435692.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSMD14-DT	ENST00000435692.6	n.344-2869T>C		intron_variant	Intron 2 of 5	5
PSMD14-DT	ENST00000628042.2	n.344-6327T>C		intron_variant	Intron 2 of 4	5
PSMD14-DT	ENST00000628613.2	n.574-6345T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103482 AN: 151910 Hom.: 35475 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.681 AC: 103532 AN: 152026 Hom.: 35488 Cov.: 32 AF XY: 0.677 AC XY: 50283 AN XY: 74318

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.684

Alfa AF: 0.705 Hom.: 73227

Bravo AF: 0.694

Asia WGS AF: 0.534 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882364; hg19: chr2-162114060;