2-161250784-G-T

Variant names:

• chr2-161250784-G-T
• rs3731769
• ENST00000421122.8:n.323+212C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421122.8(PSMD14-DT):​n.323+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 ENST00000421122.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 7 publications found

Genes affected

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

LINC01806 (HGNC:52599): (long intergenic non-protein coding RNA 1806)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421122.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14-DT	NR_110593.1		n.286+212C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14-DT	ENST00000421122.8	TSL:3	n.323+212C>A		intron	N/A
	PSMD14-DT	ENST00000435692.6	TSL:5	n.666+212C>A		intron	N/A
	PSMD14-DT	ENST00000445372.5	TSL:3	n.167+212C>A		intron	N/A

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

African (AFR) AF: 0.438 AC: 18132 AN: 41416

American (AMR) AF: 0.694 AC: 10594 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2727 AN: 5170

South Asian (SAS) AF: 0.619 AC: 2983 AN: 4816

European-Finnish (FIN) AF: 0.620 AC: 6546 AN: 10562

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.698 AC: 47405 AN: 67936

Other (OTH) AF: 0.625 AC: 1323 AN: 2116

Alfa AF: 0.669 Hom.: 91869

Bravo AF: 0.615

Asia WGS AF: 0.519 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.50
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3731769; hg19: chr2-162107295;