chr1-157519726-T-G

Position:

• chr1-157519726-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031281.3(FCRL5):​c.2660+17A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,610,896 control chromosomes in the GnomAD database, including 67,239 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 0.22 (4476 hom., cov: 32)
  • Exomes 𝑓: 0.29 (62763 hom.)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.2660+17A>C		intron_variant		ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835.8	c.2660+17A>C		intron_variant		1	NM_031281.3	ENSP00000354691	P1
FCRL5	ENST00000461387.5	n.1937+17A>C		intron_variant, non_coding_transcript_variant		2
FCRL5	ENST00000497286.5	n.1753+17A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32974 AN: 152006 Hom.: 4473 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.233

GnomAD3 exomes AF: 0.263 AC: 66103 AN: 251250 Hom.: 9768 AF XY: 0.271 AC XY: 36855 AN XY: 135774

Gnomad AFR exome AF: 0.0466

Gnomad AMR exome AF: 0.244

Gnomad ASJ exome AF: 0.370

Gnomad EAS exome AF: 0.0994

Gnomad SAS exome AF: 0.294

Gnomad FIN exome AF: 0.269

Gnomad NFE exome AF: 0.306

Gnomad OTH exome AF: 0.297

GnomAD4 exome AF: 0.287 AC: 418499 AN: 1458772 Hom.: 62763 Cov.: 32 AF XY: 0.289 AC XY: 209735 AN XY: 725928

Gnomad4 AFR exome AF: 0.0441

Gnomad4 AMR exome AF: 0.242

Gnomad4 ASJ exome AF: 0.371

Gnomad4 EAS exome AF: 0.0939

Gnomad4 SAS exome AF: 0.302

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.275

GnomAD4 genome AF: 0.217 AC: 32985 AN: 152124 Hom.: 4476 Cov.: 32 AF XY: 0.218 AC XY: 16231 AN XY: 74356

Gnomad4 AFR AF: 0.0556

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.0982

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.233

Alfa AF: 0.283 Hom.: 3375

Bravo AF: 0.207

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs1332714; hg19: chr1-157489516; COSMIC: COSV62518984; COSMIC: COSV62518984;