rs10494316

Variant summary

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

The NM_031281.3(FCRL5):​c.844+483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,024 control chromosomes in the GnomAD database, including 27,051 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 0.58 ( 27051 hom., cov: 32)

Consequence

FCRL5
NM_031281.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.27
Variant links:
Genes affected
FCRL5 (HGNC:18508): (Fc receptor like 5) This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]

Genome browser will be placed here

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=-1.02).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FCRL5NM_031281.3 linkc.844+483C>T intron_variant Intron 5 of 16 ENST00000361835.8 NP_112571.2 Q96RD9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FCRL5ENST00000361835.8 linkc.844+483C>T intron_variant Intron 5 of 16 1 NM_031281.3 ENSP00000354691.3 Q96RD9-1
FCRL5ENST00000368190.7 linkc.844+483C>T intron_variant Intron 5 of 9 1 ENSP00000357173.3 Q96RD9-3
FCRL5ENST00000368189.3 linkc.844+483C>T intron_variant Intron 5 of 7 1 ENSP00000357172.3 Q96RD9-4
FCRL5ENST00000481082.1 linkn.1042+483C>T intron_variant Intron 6 of 6 2

Frequencies

GnomAD3 genomes
AF:
0.583
AC:
88495
AN:
151906
Hom.:
27037
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.386
Gnomad AMI
AF:
0.567
Gnomad AMR
AF:
0.648
Gnomad ASJ
AF:
0.654
Gnomad EAS
AF:
0.728
Gnomad SAS
AF:
0.758
Gnomad FIN
AF:
0.678
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.646
Gnomad OTH
AF:
0.577
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.582
AC:
88540
AN:
152024
Hom.:
27051
Cov.:
32
AF XY:
0.590
AC XY:
43807
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.386
AC:
0.385612
AN:
0.385612
Gnomad4 AMR
AF:
0.649
AC:
0.648776
AN:
0.648776
Gnomad4 ASJ
AF:
0.654
AC:
0.65389
AN:
0.65389
Gnomad4 EAS
AF:
0.728
AC:
0.728135
AN:
0.728135
Gnomad4 SAS
AF:
0.757
AC:
0.757368
AN:
0.757368
Gnomad4 FIN
AF:
0.678
AC:
0.677511
AN:
0.677511
Gnomad4 NFE
AF:
0.646
AC:
0.646145
AN:
0.646145
Gnomad4 OTH
AF:
0.576
AC:
0.575758
AN:
0.575758
Heterozygous variant carriers
0
1793
3586
5378
7171
8964
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
748
1496
2244
2992
3740
<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:
0.629
Hom.:
52522
Bravo
AF:
0.568
Asia WGS
AF:
0.708
AC:
2461
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.23
DANN
Benign
0.22
Mutation Taster
=100/0
polymorphism (auto)

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10494316; hg19: chr1-157513569; API