rs483850

Variant names:

• chr1-206916626-T-A
• rs483850
• NM_005449.5:c.38-2532A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-206916626-T-A
• chr1-206916626-T-C

Variant summary

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

The NM_005449.5(FCMR):​c.38-2532A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,126 control chromosomes in the GnomAD database, including 28,662 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 0.59 (28662 hom., cov: 32)
• Consequence: FCMR NM_005449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 5 publications found

Genes affected

FCMR (HGNC:14315): (Fc mu receptor) Fc receptors specifically bind to the Fc region of immunoglobulins (Igs) to mediate the unique functions of each Ig class. FAIM3 encodes an Fc receptor for IgM (see MIM 147020) (Kubagawa et al., 2009 [PubMed 19858324]; Shima et al., 2010 [PubMed 20042454]).[supplied by OMIM, Jul 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCMR	NM_005449.5	c.38-2532A>T		intron_variant	Intron 1 of 7	ENST00000367091.8	NP_005440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCMR	ENST00000367091.8	c.38-2532A>T		intron_variant	Intron 1 of 7	1	NM_005449.5	ENSP00000356058.3

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89383 AN: 152008 Hom.: 28596 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.588 AC: 89509 AN: 152126 Hom.: 28662 Cov.: 32 AF XY: 0.578 AC XY: 42984 AN XY: 74344

African (AFR) AF: 0.862 AC: 35780 AN: 41510

American (AMR) AF: 0.541 AC: 8267 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1923 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2234 AN: 5176

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4820

European-Finnish (FIN) AF: 0.412 AC: 4358 AN: 10572

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33704 AN: 67992

Other (OTH) AF: 0.601 AC: 1268 AN: 2110

Alfa AF: 0.544 Hom.: 2793

Bravo AF: 0.612

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.79
PhyloP100		0.79
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: rs483850; hg19: chr1-207089971;