chr19-42903725-CA-C

Position:

• chr19-42903725-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000292125.6(PSG6):​c.1241-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (7166 hom., cov: 0)
  • Exomes 𝑓: 0.27 (1699 hom.)
  • Failed GnomAD Quality Control
• Consequence: PSG6 ENST00000292125.6 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.578

Genes affected

PSG6 (HGNC:9523): (pregnancy specific beta-1-glycoprotein 6) 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. The protein encoded by this gene contains the Arg-Gly-Asp tripeptide associated with cellular adhesion and recognition. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-42903725-CA-C is Benign according to our data. Variant chr19-42903725-CA-C is described in ClinVar as [Benign]. Clinvar id is 2789134.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSG6	NM_001031850.4	c.1241-1280del		intron_variant		ENST00000187910.7
PSG6	NM_002782.5	c.1241-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSG6	ENST00000187910.7	c.1241-1280del		intron_variant		1	NM_001031850.4	A2
PSG6	ENST00000292125.6	c.1241-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		P2
PSG6	ENST00000402603.8	c.962-1280del		intron_variant		5
PSG6	ENST00000599753.1	c.*598-1280del		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.365 AC: 44042 AN: 120500 Hom.: 7170 Cov.: 0

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.384

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.371

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.270 AC: 321931 AN: 1194080 Hom.: 1699 Cov.: 0 AF XY: 0.272 AC XY: 159662 AN XY: 586352

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.344

Gnomad4 ASJ exome AF: 0.334

Gnomad4 EAS exome AF: 0.358

Gnomad4 SAS exome AF: 0.367

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.254

Gnomad4 OTH exome AF: 0.291

GnomAD4 genome AF: 0.365 AC: 44044 AN: 120516 Hom.: 7166 Cov.: 0 AF XY: 0.370 AC XY: 21426 AN XY: 57986

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.368

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 30, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.21		Position offset: -4

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

Publications

LitVar

Other links and lift over

dbSNP: rs59871741; hg19: chr19-43407877;