16-74042353-A-G

Variant summary

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

The ENST00000641277.1(PSMD7-DT):n.373-25732T>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 0.431 in 151,974 control chromosomes in the GnomAD database, including 14,301 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 0.43 (14301 hom., cov: 32)
• Consequence: PSMD7-DT ENST00000641277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMD7-DT	ENST00000641277.1	n.373-25732T>C		intron_variant, non_coding_transcript_variant
PSMD7-DT	ENST00000641127.1	n.303+91288T>C		intron_variant, non_coding_transcript_variant
PSMD7-DT	ENST00000641872.1	n.482+71951T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65467 AN: 151854 Hom.: 14279 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.431 AC: 65548 AN: 151974 Hom.: 14301 Cov.: 32 AF XY: 0.436 AC XY: 32375 AN XY: 74298

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.428

Alfa AF: 0.378 Hom.: 8274

Bravo AF: 0.434

Asia WGS AF: 0.466 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2716601; hg19: chr16-74076252;