rs17416676

Variant names:

• chr1-157534015-G-A
• rs17416676
• ENST00000368189.3:c.*501C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157534015-G-A
• chr1-157534015-G-T

Variant summary

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

The ENST00000368189.3(FCRL5):​c.*501C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 178,768 control chromosomes in the GnomAD database, including 5,154 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 0.21 (4281 hom., cov: 32)
  • Exomes 𝑓: 0.25 (873 hom.)
• Consequence: FCRL5 ENST00000368189.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368189.3. 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.1681+599C>T		intron	N/A	NP_112571.2	Q96RD9-1
	FCRL5	NM_001195388.2		c.1681+599C>T		intron	N/A	NP_001182317.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	ENST00000368189.3	TSL:1	c.*501C>T		3_prime_UTR	Exon 8 of 8	ENSP00000357172.3	Q96RD9-4
	FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.1681+599C>T		intron	N/A	ENSP00000354691.3	Q96RD9-1
	FCRL5	ENST00000368190.7	TSL:1	c.1681+599C>T		intron	N/A	ENSP00000357173.3	Q96RD9-3

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32230 AN: 151948 Hom.: 4279 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.249 AC: 6644 AN: 26702 Hom.: 873 Cov.: 0 AF XY: 0.243 AC XY: 3403 AN XY: 13996

African (AFR) AF: 0.0460 AC: 25 AN: 544

American (AMR) AF: 0.220 AC: 606 AN: 2754

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 221 AN: 594

East Asian (EAS) AF: 0.0928 AC: 146 AN: 1574

South Asian (SAS) AF: 0.276 AC: 856 AN: 3106

European-Finnish (FIN) AF: 0.249 AC: 266 AN: 1070

Middle Eastern (MID) AF: 0.273 AC: 18 AN: 66

European-Non Finnish (NFE) AF: 0.265 AC: 4164 AN: 15690

Other (OTH) AF: 0.262 AC: 342 AN: 1304

GnomAD4 genome AF: 0.212 AC: 32235 AN: 152066 Hom.: 4281 Cov.: 32 AF XY: 0.212 AC XY: 15794 AN XY: 74350

African (AFR) AF: 0.0524 AC: 2176 AN: 41494

American (AMR) AF: 0.228 AC: 3487 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1461 AN: 3464

East Asian (EAS) AF: 0.106 AC: 549 AN: 5182

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2698 AN: 10558

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19795 AN: 67950

Other (OTH) AF: 0.233 AC: 490 AN: 2106

Alfa AF: 0.265 Hom.: 5940

Bravo AF: 0.204

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.6
DANN	Benign	0.50
PhyloP100		0.28
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17416676;

hg19: chr1-157503805;