16-74042353-A-G

Variant names:

• chr16-74042353-A-G
• rs2716601
• ENST00000641127.2:n.441+91288T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641127.2(PSMD7-DT):​n.441+91288T>C variant causes a intron 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 ENST00000641127.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641127.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD7-DT	ENST00000641127.2		n.441+91288T>C		intron	N/A
	PSMD7-DT	ENST00000641277.1		n.373-25732T>C		intron	N/A
	PSMD7-DT	ENST00000641872.1		n.482+71951T>C		intron	N/A

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

African (AFR) AF: 0.474 AC: 19654 AN: 41438

American (AMR) AF: 0.466 AC: 7121 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2818 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1874 AN: 4814

European-Finnish (FIN) AF: 0.453 AC: 4776 AN: 10540

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26282 AN: 67970

Other (OTH) AF: 0.428 AC: 905 AN: 2114

Alfa AF: 0.399 Hom.: 32395

Bravo AF: 0.434

Asia WGS AF: 0.466 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2716601; hg19: chr16-74076252;