1-157802090-C-T

Position:

• chr1-157802090-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_052938.5(FCRL1):​c.711G>A​(p.Pro237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 1,613,850 control chromosomes in the GnomAD database, including 203,058 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 0.41 (15189 hom., cov: 32)
  • Exomes 𝑓: 0.50 (187869 hom.)
• Consequence: FCRL1 NM_052938.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.78

Genes affected

FCRL1 (HGNC:18509): (Fc receptor like 1) This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains three extracellular C2-like immunoglobulin domains, a transmembrane domain and a cytoplasmic domain with two immunoreceptor-tyrosine activation motifs. This protein may play a role in the regulation of cancer cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP7: Synonymous conserved (PhyloP=-5.78 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL1	NM_052938.5	c.711G>A	p.Pro237=	synonymous_variant	5/11	ENST00000368176.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL1	ENST00000368176.8	c.711G>A	p.Pro237=	synonymous_variant	5/11	1	NM_052938.5	P4

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62264 AN: 151966 Hom.: 15180 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.423

GnomAD3 exomes AF: 0.494 AC: 123940 AN: 250862 Hom.: 32099 AF XY: 0.502 AC XY: 68061 AN XY: 135564

Gnomad AFR exome AF: 0.118

Gnomad AMR exome AF: 0.495

Gnomad ASJ exome AF: 0.516

Gnomad EAS exome AF: 0.542

Gnomad SAS exome AF: 0.508

Gnomad FIN exome AF: 0.584

Gnomad NFE exome AF: 0.516

Gnomad OTH exome AF: 0.514

GnomAD4 exome AF: 0.502 AC: 734195 AN: 1461766 Hom.: 187869 Cov.: 57 AF XY: 0.504 AC XY: 366767 AN XY: 727170

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.499

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.562

Gnomad4 SAS exome AF: 0.513

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.509

Gnomad4 OTH exome AF: 0.482

GnomAD4 genome AF: 0.410 AC: 62281 AN: 152084 Hom.: 15189 Cov.: 32 AF XY: 0.415 AC XY: 30834 AN XY: 74324

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.420

Alfa AF: 0.447 Hom.: 6685

Bravo AF: 0.389

Asia WGS AF: 0.448 AC: 1557 AN: 3476

EpiCase AF: 0.514

EpiControl AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.086
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs4971154; hg19: chr1-157771880; COSMIC: COSV63824383; COSMIC: COSV63824383;