Variant chr17-42574011-G-A 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.337+88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00573 in 1,572,828 control chromosomes in the GnomAD database, including 307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0057 ( 30 hom., cov: 33)

Exomes 𝑓: 0.0057 ( 277 hom. )

Consequence

PSMC3IP
NM_016556.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.830

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=-0.83).

BP6

Variant 17-42574011-G-A is Benign according to our data. Variant chr17-42574011-G-A is described in ClinVar as [Benign]. Clinvar id is 1237505.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMC3IP	NM_016556.4 link	c.337+88C>T		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.337+88C>T		intron_variant		1	NM_016556.4	ENSP00000377384.2		Q9P2W1-1

Frequencies

GnomAD3 genomes

AF:

0.00555

AC:

845

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00550

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.0206

Gnomad SAS

AF:

0.0673

Gnomad FIN

AF:

0.00537

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000573

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.0131

AC:

2463

AN:

187848

Hom.:

AF XY:

0.0161

AC XY:

1624

AN XY:

101154

show subpopulations

Gnomad AFR exome

AF:

0.00638

Gnomad AMR exome

AF:

0.000694

Gnomad ASJ exome

AF:

0.00134

Gnomad EAS exome

AF:

0.0210

Gnomad SAS exome

AF:

0.0716

Gnomad FIN exome

AF:

0.00682

Gnomad NFE exome

AF:

0.000900

Gnomad OTH exome

AF:

0.00732

GnomAD4 exome

AF:

0.00573

AC:

8143

AN:

1420530

Hom.:

277

Cov.:

AF XY:

0.00754

AC XY:

5303

AN XY:

703552

show subpopulations

Gnomad4 AFR exome

AF:

0.00596

Gnomad4 AMR exome

AF:

0.00102

Gnomad4 ASJ exome

AF:

0.000788

Gnomad4 EAS exome

AF:

0.0275

Gnomad4 SAS exome

AF:

0.0675

Gnomad4 FIN exome

AF:

0.00637

Gnomad4 NFE exome

AF:

0.000487

Gnomad4 OTH exome

AF:

0.00814

GnomAD4 genome

AF:

0.00567

AC:

864

AN:

152298

Hom.:

Cov.:

AF XY:

0.00683

AC XY:

509

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00551

Gnomad4 AMR

AF:

0.00477

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.0208

Gnomad4 SAS

AF:

0.0673

Gnomad4 FIN

AF:

0.00537

Gnomad4 NFE

AF:

0.000573

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00191

Hom.:

Bravo

AF:

0.00406

Asia WGS

AF:

0.0730

AC:

252

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	Jun 05, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.2

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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