ENST00000527084.5:c.-183+5024C>G

Variant names:

• chr1-247512257-C-G
• rs7550918
• ENST00000527084.5:c.-183+5024C>G

Variant summary

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

The ENST00000527084.5(GCSAML):​c.-183+5024C>G variant causes a intron 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: 28)
• Consequence: GCSAML ENST00000527084.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 20 publications found

Genes affected

GCSAML (HGNC:29583): (germinal center associated signaling and motility like) This gene encodes a protein thought to be a signaling molecule associated with germinal centers, the sites of proliferation and differentiation of mature B lymphocytes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ENSG00000302135 (HGNC:):

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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCSAML	NM_001281853.1	c.-172+5024C>G		intron_variant	Intron 1 of 6		NP_001268782.1
GCSAML	NM_001281834.2	c.-379+5024C>G		intron_variant	Intron 1 of 6		NP_001268763.1
GCSAML	NM_001281835.2	c.-263+5024C>G		intron_variant	Intron 1 of 5		NP_001268764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCSAML	ENST00000527084.5	c.-183+5024C>G		intron_variant	Intron 1 of 5	1		ENSP00000432118.1
GCSAML	ENST00000527541.5	c.-123+5024C>G		intron_variant	Intron 1 of 4	1		ENSP00000435110.1
GCSAML	ENST00000536561.5	c.-172+5024C>G		intron_variant	Intron 1 of 6	4		ENSP00000446460.2

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 54004

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.42
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: rs7550918; hg19: chr1-247675559;