rs10494316

Variant names:

• chr1-157543779-G-A
• rs10494316
• NM_031281.3:c.844+483C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157543779-G-A
• chr1-157543779-G-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.844+483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,024 control chromosomes in the GnomAD database, including 27,051 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 0.58 (27051 hom., cov: 32)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	NM_031281.3	MANE Select	c.844+483C>T		intron	N/A	NP_112571.2	Q96RD9-1
	FCRL5	NM_001195388.2		c.844+483C>T		intron	N/A	NP_001182317.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.844+483C>T		intron	N/A	ENSP00000354691.3	Q96RD9-1
	FCRL5	ENST00000368190.7	TSL:1	c.844+483C>T		intron	N/A	ENSP00000357173.3	Q96RD9-3
	FCRL5	ENST00000368189.3	TSL:1	c.844+483C>T		intron	N/A	ENSP00000357172.3	Q96RD9-4

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88495 AN: 151906 Hom.: 27037 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.582 AC: 88540 AN: 152024 Hom.: 27051 Cov.: 32 AF XY: 0.590 AC XY: 43807 AN XY: 74304

African (AFR) AF: 0.386 AC: 15979 AN: 41438

American (AMR) AF: 0.649 AC: 9912 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2269 AN: 3470

East Asian (EAS) AF: 0.728 AC: 3763 AN: 5168

South Asian (SAS) AF: 0.757 AC: 3649 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7164 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43912 AN: 67960

Other (OTH) AF: 0.576 AC: 1216 AN: 2112

Alfa AF: 0.629 Hom.: 52522

Bravo AF: 0.568

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.22
PhyloP100		-3.3
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: rs10494316; hg19: chr1-157513569;