Variant 17-42573781-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016556.4(PSMC3IP):c.338-158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 1,499,422 control chromosomes in the GnomAD database, including 228,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20671 hom., cov: 33)

Exomes 𝑓: 0.55 ( 207691 hom. )

Consequence

PSMC3IP
NM_016556.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0110

Variant links:

Genes affected

PSMC3IP (HGNC:17928): (PSMC3 interacting protein) This gene encodes a protein that functions in meiotic recombination. It is a subunit of the PSMC3IP/MND1 complex, which interacts with PSMC3/TBP1 to stimulate DMC1- and RAD51-mediated strand exchange during meiosis. The protein encoded by this gene can also co-activate ligand-driven transcription mediated by estrogen, androgen, glucocorticoid, progesterone, and thyroid nuclear receptors. Mutations in this gene cause XX female gonadal dysgenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2011]

PSMC3IP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 17-42573781-C-T is Benign according to our data. Variant chr17-42573781-C-T is described in ClinVar as [Benign]. Clinvar id is 1243811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMC3IP	NM_016556.4 link	c.338-158G>A		intron_variant		ENST00000393795.8	NP_057640.1	Q9P2W1-1A0A158RUX1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMC3IP	ENST00000393795.8 link	c.338-158G>A		intron_variant		1	NM_016556.4	ENSP00000377384.2		Q9P2W1-1

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

79007

AN:

151976

Hom.:

20644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.390

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.644

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.490

GnomAD3 exomes

AF:

0.535

AC:

68788

AN:

128650

Hom.:

18650

AF XY:

0.544

AC XY:

37745

AN XY:

69436

show subpopulations

Gnomad AFR exome

AF:

0.492

Gnomad AMR exome

AF:

0.519

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.439

Gnomad SAS exome

AF:

0.637

Gnomad FIN exome

AF:

0.525

Gnomad NFE exome

AF:

0.550

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.553

AC:

745309

AN:

1347328

Hom.:

207691

Cov.:

AF XY:

0.555

AC XY:

368930

AN XY:

664802

show subpopulations

Gnomad4 AFR exome

AF:

0.484

Gnomad4 AMR exome

AF:

0.518

Gnomad4 ASJ exome

AF:

0.390

Gnomad4 EAS exome

AF:

0.454

Gnomad4 SAS exome

AF:

0.635

Gnomad4 FIN exome

AF:

0.539

Gnomad4 NFE exome

AF:

0.560

Gnomad4 OTH exome

AF:

0.530

GnomAD4 genome

AF:

0.520

AC:

79077

AN:

152094

Hom.:

20671

Cov.:

AF XY:

0.517

AC XY:

38461

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.390

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.642

Gnomad4 FIN

AF:

0.531

Gnomad4 NFE

AF:

0.549

Gnomad4 OTH

AF:

0.495

Alfa

AF:

0.527

Hom.:

27398

Bravo

AF:

0.510

Asia WGS

AF:

0.589

AC:

2048

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 17, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.4

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over