19-42927865-A-C

Variant names:

• chr19-42927865-A-C
• rs2159027
• NM_002783.3:c.710-1149T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PSG7	NM_002783.3	c.710-1149T>G		intron_variant	Intron 3 of 5	ENST00000406070.7	NP_002774.2
PSG7	NM_001206650.2	c.344-1149T>G		intron_variant	Intron 2 of 4		NP_001193579.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSG7	ENST00000406070.7	c.710-1149T>G		intron_variant	Intron 3 of 5	1	NM_002783.3	ENSP00000421986.1
PSG7	ENST00000623675.3	c.344-1149T>G		intron_variant	Intron 2 of 4	1		ENSP00000485117.1
PSG7	ENST00000446844.3	c.710-1149T>G		intron_variant	Intron 3 of 4	5		ENSP00000470856.1

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

African (AFR) AF: 0.982 AC: 40513 AN: 41240

American (AMR) AF: 0.923 AC: 13979 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3295 AN: 3460

East Asian (EAS) AF: 1.00 AC: 5124 AN: 5124

South Asian (SAS) AF: 0.988 AC: 4681 AN: 4740

European-Finnish (FIN) AF: 0.909 AC: 9581 AN: 10538

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61663 AN: 67840

Other (OTH) AF: 0.927 AC: 1957 AN: 2110

Alfa AF: 0.919 Hom.: 84162

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
PhyloP100		-1.1

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

Other links and lift over

dbSNP: rs2159027; hg19: chr19-43432017;