Genetic Variant NM_031282.3:c.*464G>A (chr1-157575060-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031282.3(FCRL4):c.*464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 253,318 control chromosomes in the GnomAD database, including 19,239 homozygotes. 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: 𝑓 0.33 ( 10177 hom., cov: 33)

Exomes 𝑓: 0.40 ( 9062 hom. )

Consequence

FCRL4
NM_031282.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.373

Publications

15 publications found

Variant links:

Genes affected

FCRL4 (HGNC:18507): (Fc receptor like 4) 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 three immune-receptor tyrosine-based inhibitory motifs. This protein may play a role in the function of memory B-cells in the epithelia. Aberrations in the chromosomal region encoding this gene are associated with non-Hodgkin lymphoma and multiple myeloma. [provided by RefSeq, Apr 2009]

FCRL4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL4	NM_031282.3 link	c.*464G>A		3_prime_UTR_variant	Exon 12 of 12	ENST00000271532.2	NP_112572.1	Q96PJ5-1
FCRL4	XM_011510034.2 link	c.*464G>A		3_prime_UTR_variant	Exon 12 of 12		XP_011508336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL4	ENST00000271532.2 link	c.*464G>A		3_prime_UTR_variant	Exon 12 of 12	1	NM_031282.3	ENSP00000271532.1		Q96PJ5-1
FCRL4	ENST00000448509.6 link	n.1980G>A		non_coding_transcript_exon_variant	Exon 9 of 9	2

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49891

AN:

152004

Hom.:

10173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0846

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.342

GnomAD4 exome

AF:

0.405

AC:

40946

AN:

101196

Hom.:

9062

Cov.:

AF XY:

0.405

AC XY:

19499

AN XY:

48102

show subpopulations

African (AFR)

AF:

0.0806

AC:

314

AN:

3896

American (AMR)

AF:

0.519

AC:

2724

AN:

5246

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1851

AN:

4964

East Asian (EAS)

AF:

0.600

AC:

7032

AN:

11724

South Asian (SAS)

AF:

0.472

AC:

1714

AN:

3630

European-Finnish (FIN)

AF:

0.435

AC:

442

AN:

1016

Middle Eastern (MID)

AF:

0.332

AC:

183

AN:

552

European-Non Finnish (NFE)

AF:

0.381

AC:

23878

AN:

62608

Other (OTH)

AF:

0.371

AC:

2808

AN:

7560

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1160

2321

3481

4642

5802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

190

380

570

760

950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.328

AC:

49895

AN:

152122

Hom.:

10177

Cov.:

AF XY:

0.338

AC XY:

25137

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0844

AC:

3505

AN:

41528

American (AMR)

AF:

0.456

AC:

6969

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

1256

AN:

3468

East Asian (EAS)

AF:

0.614

AC:

3175

AN:

5172

South Asian (SAS)

AF:

0.493

AC:

2375

AN:

4814

European-Finnish (FIN)

AF:

0.453

AC:

4797

AN:

10594

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.392

AC:

26642

AN:

67956

Other (OTH)

AF:

0.338

AC:

714

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1542

3085

4627

6170

7712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.374

Hom.:

14580

Bravo

AF:

0.316

Asia WGS

AF:

0.516

AC:

1794

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.3

(source)

DANN

Benign

0.52

PhyloP100

-0.37

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over