rs1866559

Variant names:

• chr2-27112718-T-A
• rs1866559
• NM_006569.6:c.-12+6128A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-27112718-T-A
• chr2-27112718-T-C

Variant summary

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

The NM_006569.6(CGREF1):​c.-12+6128A>T 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: 33)
• Consequence: CGREF1 NM_006569.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 11 publications found

Genes affected

CGREF1 (HGNC:16962): (cell growth regulator with EF-hand domain 1) Predicted to enable calcium ion binding activity. Predicted to be involved in negative regulation of cell population proliferation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC124907744 (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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006569.6. 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
	CGREF1	NM_006569.6	MANE Select	c.-12+6128A>T		intron	N/A	NP_006560.3
	CGREF1	NM_001166239.2		c.-12+6057A>T		intron	N/A	NP_001159711.1	Q99674-4
	CGREF1	NM_001166240.2		c.-12+6128A>T		intron	N/A	NP_001159712.1	Q99674-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CGREF1	ENST00000402394.6	TSL:2 MANE Select	c.-12+6128A>T		intron	N/A	ENSP00000385452.1	Q99674-4
	CGREF1	ENST00000312734.8	TSL:5	c.-307-1750A>T		intron	N/A	ENSP00000324025.4	Q99674-4
	CGREF1	ENST00000405600.5	TSL:4	c.-12+6057A>T		intron	N/A	ENSP00000386113.1	Q99674-4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 13795

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		-0.017

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: rs1866559; hg19: chr2-27335586;