2-161257549-A-G

Variant names:

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

Variant summary

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

The ENST00000652531.2(PSMD14-DT):​n.246-6327T>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 ENST00000652531.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652531.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14-DT	ENST00000435692.6	TSL:5	n.344-2869T>C		intron	N/A
	PSMD14-DT	ENST00000628042.2	TSL:5	n.344-6327T>C		intron	N/A
	PSMD14-DT	ENST00000628613.2	TSL:5	n.574-6345T>C		intron	N/A

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

African (AFR) AF: 0.651 AC: 26998 AN: 41450

American (AMR) AF: 0.726 AC: 11100 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2535 AN: 3464

East Asian (EAS) AF: 0.532 AC: 2754 AN: 5172

South Asian (SAS) AF: 0.627 AC: 3020 AN: 4818

European-Finnish (FIN) AF: 0.623 AC: 6586 AN: 10564

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.710 AC: 48248 AN: 67964

Other (OTH) AF: 0.684 AC: 1444 AN: 2110

Alfa AF: 0.703 Hom.: 116606

Bravo AF: 0.694

Asia WGS AF: 0.534 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1882364; hg19: chr2-162114060;