rs2159027

Positions:

• chr19-42927865-A-C
• chr19-42927865-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002783.3(PSG7):​c.710-1149T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 151,402 control chromosomes in the GnomAD database, including 66,744 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 0.94 (66744 hom., cov: 31)
• Consequence: PSG7 NM_002783.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSG7	NM_002783.3	c.710-1149T>G		intron_variant		ENST00000406070.7	NP_002774.2
PSG7	NM_001206650.2	c.344-1149T>G		intron_variant			NP_001193579.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSG7	ENST00000406070.7	c.710-1149T>G		intron_variant		1	NM_002783.3	ENSP00000421986	A2
PSG7	ENST00000623675.3	c.344-1149T>G		intron_variant		1		ENSP00000485117
PSG7	ENST00000446844.3	c.710-1149T>G		intron_variant		5		ENSP00000470856	P4

Frequencies

GnomAD3 genomes AF: 0.937 AC: 141730 AN: 151288 Hom.: 66683 Cov.: 31

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.926

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.937 AC: 141849 AN: 151402 Hom.: 66744 Cov.: 31 AF XY: 0.937 AC XY: 69348 AN XY: 73972

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.927

Alfa AF: 0.916 Hom.: 64252

Bravo AF: 0.939

Asia WGS AF: 0.992 AC: 3438 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs2159027; hg19: chr19-43432017;