Variant 19-42925830-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_002783.3(PSG7):c.1186G>C(p.Val396Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,612,038 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0021 ( 9 hom., cov: 32)

Exomes 𝑓: 0.00025 ( 14 hom. )

Consequence

PSG7
NM_002783.3 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.122

Variant links:

Genes affected

PSG7 (HGNC:9524): (pregnancy specific beta-1-glycoprotein 7) This gene is a member of the pregnancy-specific glycoprotein (PSG) gene family. The PSG genes are a subgroup of the carcinoembryonic antigen (CEA) family of immunoglobulin-like genes, and are found in a gene cluster at 19q13.1-q13.2 telomeric to another cluster of CEA-related genes. The PSG genes are expressed by placental trophoblasts and released into the maternal circulation during pregnancy, and are thought to be essential for maintenance of normal pregnancy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

PSG7 links:

PSG7 (HGNC:):

PSG7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008730382).

BP6

Variant 19-42925830-C-G is Benign according to our data. Variant chr19-42925830-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 722978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSG7	NM_002783.3 linkuse as main transcript	c.1186G>C	p.Val396Leu	missense_variant	5/6	ENST00000406070.7	NP_002774.2	Q13046
PSG7	NM_001206650.2 linkuse as main transcript	c.820G>C	p.Val274Leu	missense_variant	4/5		NP_001193579.1	A0A096LNM5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PSG7	ENST00000406070.7 linkuse as main transcript	c.1186G>C	p.Val396Leu	missense_variant	5/6	1	NM_002783.3	ENSP00000421986.1	Q13046
PSG7	ENST00000623675.3 linkuse as main transcript	c.820G>C	p.Val274Leu	missense_variant	4/5	1		ENSP00000485117.1	A0A096LNM5
PSG7	ENST00000446844.3 linkuse as main transcript	c.1186G>C	p.Val396Leu	missense_variant	5/5	5		ENSP00000470856.1	A0A087WT09
PSG7	ENST00000599226.2 linkuse as main transcript	n.1748G>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00211

AC:

319

AN:

151466

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00692

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00172

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000423

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000589

Gnomad OTH

AF:

0.000961

GnomAD3 exomes

AF:

0.000562

AC:

141

AN:

250878

Hom.:

AF XY:

0.000361

AC XY:

AN XY:

135562

show subpopulations

Gnomad AFR exome

AF:

0.00757

Gnomad AMR exome

AF:

0.000260

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000985

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000353

Gnomad OTH exome

AF:

0.000327

GnomAD4 exome

AF:

0.000250

AC:

365

AN:

1460456

Hom.:

Cov.:

AF XY:

0.000216

AC XY:

157

AN XY:

726488

show subpopulations

Gnomad4 AFR exome

AF:

0.00843

Gnomad4 AMR exome

AF:

0.000268

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000815

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000153

Gnomad4 OTH exome

AF:

0.000763

GnomAD4 genome

AF:

0.00210

AC:

319

AN:

151582

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

164

AN XY:

74070

show subpopulations

Gnomad4 AFR

AF:

0.00692

Gnomad4 AMR

AF:

0.00171

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000212

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000589

Gnomad4 OTH

AF:

0.000951

Alfa

AF:

0.00154

Hom.:

Bravo

AF:

0.00286

ESP6500AA

AF:

0.00841

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.000668

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.10

CADD

Benign

9.8

DANN

Benign

0.92

DEOGEN2

Benign

0.016

T;.;.

FATHMM_MKL

Benign

0.0096

LIST_S2

Uncertain

0.95

D;D;D

MetaRNN

Benign

0.0087

T;T;T

PrimateAI

Benign

0.34

Sift4G

Uncertain

0.030

D;D;D

Polyphen

0.16

B;.;.

Vest4

0.37

MVP

0.030

GERP RS

-2.2

Varity_R

0.051

gMVP

0.060

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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