chr2-161257549-A-G

Position:

• chr2-161257549-A-G

Variant summary

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

The ENST00000652531.1(PSMD14-DT):​n.246-6327T>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 0.681 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 ENST00000652531.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD14-DT	ENST00000652531.1	n.246-6327T>C		intron_variant, non_coding_transcript_variant

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;