16-74054192-T-G

Position:

• chr16-74054192-T-G

Variant summary

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

The ENST00000641277.1(PSMD7-DT):​n.373-37571A>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 0.283 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 ENST00000641277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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=-0.88).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD7-DT	ENST00000641277.1	n.373-37571A>C		intron_variant, non_coding_transcript_variant
PSMD7-DT	ENST00000569389.5	n.804A>C		non_coding_transcript_exon_variant	3/3	3
PSMD7-DT	ENST00000641127.1	n.303+79449A>C		intron_variant, non_coding_transcript_variant
PSMD7-DT	ENST00000641872.1	n.482+60112A>C		intron_variant, non_coding_transcript_variant

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;