rs3811035

Variant names:

• chr1-157515771-G-A
• rs3811035
• NM_031281.3:c.2845-7C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157515771-G-A
• chr1-157515771-G-C
• chr1-157515771-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031281.3(FCRL5):​c.2845-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 1,613,542 control chromosomes in the GnomAD database, including 327,006 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (23970 hom., cov: 32)
  • Exomes 𝑓: 0.64 (303036 hom.)
• Consequence: FCRL5 NM_031281.3 splice_region, intron
• Scores: Splicing: ADA: 0.00002593
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 19 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.2845-7C>T		splice_region_variant, intron_variant	Intron 16 of 16	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835.8	c.2845-7C>T		splice_region_variant, intron_variant	Intron 16 of 16	1	NM_031281.3	ENSP00000354691.3
FCRL5	ENST00000461387.5	n.2122-7C>T		splice_region_variant, intron_variant	Intron 6 of 6	2
FCRL5	ENST00000462218.1	n.233-7C>T		splice_region_variant, intron_variant	Intron 1 of 1	2
FCRL5	ENST00000497286.5	n.1938-7C>T		splice_region_variant, intron_variant	Intron 8 of 8	2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78579 AN: 151818 Hom.: 23959 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.531

GnomAD2 exomes AF: 0.634 AC: 159414 AN: 251336 AF XY: 0.642

Gnomad AFR exome AF: 0.151

Gnomad AMR exome AF: 0.720

Gnomad ASJ exome AF: 0.623

Gnomad EAS exome AF: 0.653

Gnomad FIN exome AF: 0.690

Gnomad NFE exome AF: 0.656

Gnomad OTH exome AF: 0.648

GnomAD4 exome AF: 0.638 AC: 932433 AN: 1461604 Hom.: 303036 Cov.: 52 AF XY: 0.640 AC XY: 465658 AN XY: 727120

African (AFR) AF: 0.145 AC: 4842 AN: 33474

American (AMR) AF: 0.712 AC: 31857 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 16322 AN: 26136

East Asian (EAS) AF: 0.656 AC: 26040 AN: 39700

South Asian (SAS) AF: 0.666 AC: 57441 AN: 86254

European-Finnish (FIN) AF: 0.687 AC: 36647 AN: 53370

Middle Eastern (MID) AF: 0.564 AC: 3250 AN: 5764

European-Non Finnish (NFE) AF: 0.647 AC: 719076 AN: 1111794

Other (OTH) AF: 0.612 AC: 36958 AN: 60394

GnomAD4 genome AF: 0.517 AC: 78598 AN: 151938 Hom.: 23970 Cov.: 32 AF XY: 0.527 AC XY: 39110 AN XY: 74236

African (AFR) AF: 0.167 AC: 6943 AN: 41468

American (AMR) AF: 0.639 AC: 9765 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3361 AN: 5136

South Asian (SAS) AF: 0.689 AC: 3315 AN: 4812

European-Finnish (FIN) AF: 0.673 AC: 7101 AN: 10550

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44196 AN: 67916

Other (OTH) AF: 0.528 AC: 1114 AN: 2110

Alfa AF: 0.608 Hom.: 63231

Bravo AF: 0.498

Asia WGS AF: 0.630 AC: 2187 AN: 3478

EpiCase AF: 0.640

EpiControl AF: 0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000026
dbscSNV1_RF	Benign	0.0
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: rs3811035; hg19: chr1-157485561;