chr1-157517598-T-C

Variant names:

• chr1-157517598-T-C
• rs6692977
• NM_031281.3:c.2812+831A>G

Variant summary

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

The NM_031281.3(FCRL5):​c.2812+831A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,956 control chromosomes in the GnomAD database, including 35,372 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 0.68 (35372 hom., cov: 30)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.2812+831A>G		intron_variant	Intron 15 of 16	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835.8	c.2812+831A>G		intron_variant	Intron 15 of 16	1	NM_031281.3	ENSP00000354691.3
FCRL5	ENST00000461387.5	n.2089+831A>G		intron_variant	Intron 5 of 6	2
FCRL5	ENST00000497286.5	n.1905+831A>G		intron_variant	Intron 7 of 8	2

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103101 AN: 151838 Hom.: 35325 Cov.: 30

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.679 AC: 103202 AN: 151956 Hom.: 35372 Cov.: 30 AF XY: 0.686 AC XY: 50928 AN XY: 74272

African (AFR) AF: 0.644 AC: 26693 AN: 41426

American (AMR) AF: 0.689 AC: 10516 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4706 AN: 5162

South Asian (SAS) AF: 0.789 AC: 3789 AN: 4802

European-Finnish (FIN) AF: 0.710 AC: 7488 AN: 10550

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45576 AN: 67972

Other (OTH) AF: 0.660 AC: 1392 AN: 2110

Alfa AF: 0.677 Hom.: 4136

Bravo AF: 0.674

Asia WGS AF: 0.805 AC: 2797 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	1.2
DANN	Benign	0.35
PhyloP100		-0.17
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: rs6692977; hg19: chr1-157487388;