rs12325114

Variant names:

• chr16-74269992-T-C
• rs12325114
• ENST00000562888.2:n.351+26423A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-74269992-T-C
• chr16-74269992-T-G

Variant summary

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

The ENST00000562888.2(PSMD7-DT):​n.351+26423A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,106 control chromosomes in the GnomAD database, including 1,468 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 0.14 (1468 hom., cov: 32)
• Consequence: PSMD7-DT ENST00000562888.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 6 publications found

Genes affected

PSMD7-DT (HGNC:53056): (PSMD7 divergent transcript)

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 (EAS) allele frequency at 95% confidence interval = 0.221 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
PSMD7-DT	ENST00000562888.2	n.351+26423A>G		intron_variant	Intron 1 of 2	5
PSMD7-DT	ENST00000569389.5	n.129+26631A>G		intron_variant	Intron 1 of 2	3
PSMD7-DT	ENST00000641127.2	n.138+26631A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20871 AN: 151988 Hom.: 1467 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.137 AC: 20886 AN: 152106 Hom.: 1468 Cov.: 32 AF XY: 0.138 AC XY: 10279 AN XY: 74348

African (AFR) AF: 0.0999 AC: 4148 AN: 41512

American (AMR) AF: 0.146 AC: 2226 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 709 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1195 AN: 5160

South Asian (SAS) AF: 0.0751 AC: 362 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10566

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.140 AC: 9531 AN: 67988

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.101 Hom.: 246

Bravo AF: 0.135

Asia WGS AF: 0.190 AC: 663 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	1.0
DANN	Benign	0.34
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs12325114; hg19: chr16-74303891;