rs11649339

chr16-74238831-A-C

Variant summary

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

The ENST00000641277.1(PSMD7-DT):n.112-32666T>G 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 0.147 in 152,204 control chromosomes in the GnomAD database, including 1,649 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 0.15 (1649 hom., cov: 32)
• Consequence: PSMD7-DT ENST00000641277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

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=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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.112-32666T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22409 AN: 152086 Hom.: 1648 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.147 AC: 22430 AN: 152204 Hom.: 1649 Cov.: 32 AF XY: 0.148 AC XY: 10996 AN XY: 74392

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.147

Alfa AF: 0.144 Hom.: 344

Bravo AF: 0.146

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	3.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11649339; hg19: chr16-74272730;