rs483850

chr1-206916626-T-Achr1-206916626-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FCMR	NM_005449.5	c.38-2532A>T		intron_variant		ENST00000367091.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCMR	ENST00000367091.8	c.38-2532A>T		intron_variant		1	NM_005449.5	P2

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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.601

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

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: rs483850; hg19: chr1-207089971;