1-157768448-AGG-GGT

Variant names:

• chr1-157768448-AGG-GGT
• NM_030764.4:c.847_849delCCTinsACC
• FCRL2 p.Pro283Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_030764.4(FCRL2):​c.847_849delCCTinsACC​(p.Pro283Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P283S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FCRL2 NM_030764.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 0 publications found

Genes affected

FCRL2 (HGNC:14875): (Fc receptor like 2) This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein has four extracellular C2-type immunoglobulin domains, a transmembrane domain and a cytoplasmic domain that contains one immunoreceptor-tyrosine activation motif and two immunoreceptor-tyrosine inhibitory motifs. This protein may be a prognostic marker for chronic lymphocytic leukemia. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Apr 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030764.4. 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
	FCRL2	NM_030764.4	MANE Select	c.847_849delCCTinsACC	p.Pro283Thr	missense	N/A	NP_110391.2
	FCRL2	NM_001159488.2		c.847_849delCCTinsACC	p.Pro283Thr	missense	N/A	NP_001152960.1	B4DVJ9
	FCRL2	NR_125358.2		n.370-1479_370-1477delCCTinsACC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL2	ENST00000361516.8	TSL:1 MANE Select	c.847_849delCCTinsACC	p.Pro283Thr	missense	N/A	ENSP00000355157.3	Q96LA5-1
	FCRL2	ENST00000368181.4	TSL:1	c.311-1479_311-1477delCCTinsACC		intron	N/A	ENSP00000357163.4	Q96LA5-5
	FCRL2	ENST00000368178.3	TSL:1	n.1861_1863delCCTinsACC		non_coding_transcript_exon	Exon 1 of 7

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-157738238;