chr16-74054192-T-G

Variant names:

• chr16-74054192-T-G
• rs2387084
• ENST00000569389.5:n.804A>C

Variant summary

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

The ENST00000569389.5(PSMD7-DT):​n.804A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,022 control chromosomes in the GnomAD database, including 6,348 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 0.28 (6348 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: PSMD7-DT ENST00000569389.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

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

ENSG00000279420 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 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	ENST00000569389.5	n.804A>C		non_coding_transcript_exon_variant	Exon 3 of 3	3
PSMD7-DT	ENST00000641127.1	n.303+79449A>C		intron_variant	Intron 2 of 3
PSMD7-DT	ENST00000641277.1	n.373-37571A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42977 AN: 151892 Hom.: 6345 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 NFE exome AF: 0.200

GnomAD4 genome AF: 0.283 AC: 43003 AN: 152010 Hom.: 6348 Cov.: 31 AF XY: 0.283 AC XY: 21054 AN XY: 74334

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.277

Alfa AF: 0.277 Hom.: 6290

Bravo AF: 0.284

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2387084; hg19: chr16-74088091;