chr1-157519517-G-A

Variant names:

• chr1-157519517-G-A
• rs3811033
• NM_031281.3:c.2660+226C>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.2660+226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,156 control chromosomes in the GnomAD database, including 1,692 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 0.13 (1692 hom., cov: 32)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031281.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	NM_031281.3	MANE Select	c.2660+226C>T		intron	N/A	NP_112571.2
	FCRL5	NM_001195388.2		c.2660+226C>T		intron	N/A	NP_001182317.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.2660+226C>T		intron	N/A	ENSP00000354691.3
	FCRL5	ENST00000461387.5	TSL:2	n.1937+226C>T		intron	N/A
	FCRL5	ENST00000497286.5	TSL:2	n.1753+226C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20003 AN: 152038 Hom.: 1694 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.131 AC: 19991 AN: 152156 Hom.: 1692 Cov.: 32 AF XY: 0.130 AC XY: 9653 AN XY: 74378

African (AFR) AF: 0.0342 AC: 1422 AN: 41524

American (AMR) AF: 0.124 AC: 1898 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3472

East Asian (EAS) AF: 0.0941 AC: 487 AN: 5178

South Asian (SAS) AF: 0.144 AC: 695 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10572

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12121 AN: 67994

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.159 Hom.: 1560

Bravo AF: 0.122

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.41
PhyloP100		-0.89
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

Other links and lift over

dbSNP: rs3811033; hg19: chr1-157489307;