19-43193077-G-T

Variant names:

• chr19-43193077-G-T
• rs8603
• NM_002780.5:c.*295C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002780.5(PSG4):​c.*295C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: PSG4 NM_002780.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

Genes affected

PSG4 (HGNC:9521): (pregnancy specific beta-1-glycoprotein 4) The protein encoded by this gene is a pregnancy-specific glycoprotein (PSG), one of several encoded by a cluster of similar genes on chromosome 19. This gene is a member of the carcinoembryonic antigen (CEA) gene family and may play a role in regulation of the innate immune system. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002780.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSG4	NM_002780.5	MANE Select	c.*295C>A		3_prime_UTR	Exon 6 of 6	NP_002771.2
	PSG4	NM_001276495.2		c.*295C>A		3_prime_UTR	Exon 5 of 5	NP_001263424.1	Q00888-3
	PSG4	NM_213633.3		c.*295C>A		3_prime_UTR	Exon 5 of 5	NP_998798.1	Q00888-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSG4	ENST00000405312.8	TSL:1 MANE Select	c.*295C>A		3_prime_UTR	Exon 6 of 6	ENSP00000384770.3	Q00888-1
	PSG4	ENST00000244295.13	TSL:1	c.*295C>A		3_prime_UTR	Exon 5 of 5	ENSP00000244295.8	Q00888-2
	PSG4	ENST00000433626.6	TSL:2	c.*295C>A		3_prime_UTR	Exon 5 of 5	ENSP00000387864.2	Q00888-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.21
PhyloP100		-1.0

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: rs8603; hg19: chr19-43697229;