dbSNP rs1649583502: FCRL2:p.Val339Ile (chr1-157767378-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_030764.4(FCRL2):c.1015G>A(p.Val339Ile) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)

Consequence

FCRL2
NM_030764.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.868

Publications

0 publications found

Variant links:

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]

FCRL2 links:

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ACMG classification

Classification was made for transcript

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 (MetaRNN=0.10449314).

BP6

Variant 1-157767378-C-T is Benign according to our data. Variant chr1-157767378-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2225982.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FCRL2	NM_030764.4	MANE Select	c.1015G>A	p.Val339Ile	missense	Exon 6 of 12	NP_110391.2
FCRL2	NM_001159488.2		c.1015G>A	p.Val339Ile	missense	Exon 6 of 9	NP_001152960.1	B4DVJ9
FCRL2	NR_125358.2		n.370-407G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FCRL2	ENST00000361516.8	TSL:1 MANE Select	c.1015G>A	p.Val339Ile	missense	Exon 6 of 12	ENSP00000355157.3	Q96LA5-1
FCRL2	ENST00000469986.1	TSL:1	c.256G>A	p.Val86Ile	missense	Exon 1 of 2	ENSP00000417393.1	Q96LA5-3
FCRL2	ENST00000368181.4	TSL:1	c.311-407G>A		intron	N/A	ENSP00000357163.4	Q96LA5-5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.5

(source)

DANN

Benign

0.67

DEOGEN2

Benign

0.017

Eigen

Benign

-0.94

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0077

LIST_S2

Benign

0.66

M_CAP

Benign

0.0030

MetaRNN

Benign

0.10

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.5

PhyloP100

-0.87

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.60

REVEL

Benign

0.031

Sift

Benign

0.35

Sift4G

Benign

0.12

Polyphen

0.73

Vest4

0.13

MutPred

0.32

Loss of glycosylation at S344 (P = 0.2034)

MVP

0.13

MPC

0.040

ClinPred

0.49

GERP RS

-1.6

PromoterAI

-0.022

Neutral

(source)

Varity_R

0.023

gMVP

0.059

Mutation Taster

=100/0

polymorphism

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over