ENST00000569389.5:n.804A>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000279420 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000641127.2	n.441+79449A>C		intron_variant	Intron 3 of 4
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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.264 AC: 10956 AN: 41444

American (AMR) AF: 0.291 AC: 4449 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 924 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2385 AN: 5162

South Asian (SAS) AF: 0.287 AC: 1380 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10566

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19322 AN: 67972

Other (OTH) AF: 0.277 AC: 583 AN: 2104

Alfa AF: 0.281 Hom.: 9261

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2387084; hg19: chr16-74088091;