chr1-157519517-G-A

Position:

• chr1-157519517-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.2660+226C>T		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+226C>T		intron_variant		1	NM_031281.3	ENSP00000354691	P1
FCRL5	ENST00000461387.5	n.1937+226C>T		intron_variant, non_coding_transcript_variant		2
FCRL5	ENST00000497286.5	n.1753+226C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.162

Alfa AF: 0.161 Hom.: 1144

Bravo AF: 0.122

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs3811033; hg19: chr1-157489307;