NM_001405862.1:c.-36-388G>C

Variant names:

• chr1-206922278-C-G
• rs291084
• NM_001405862.1:c.-36-388G>C

Variant summary

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

The NM_001405862.1(FCMR):​c.-36-388G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,992 control chromosomes in the GnomAD database, including 12,301 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 0.39 (12301 hom., cov: 32)
• Consequence: FCMR NM_001405862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCMR	NM_001405862.1	c.-36-388G>C		intron_variant	Intron 1 of 9		NP_001392791.1
FCMR	NM_001405871.1	c.-36-388G>C		intron_variant	Intron 1 of 8		NP_001392800.1
FCMR	NM_001405864.1	c.-36-388G>C		intron_variant	Intron 1 of 7		NP_001392793.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCMR	ENST00000525793.5	c.-91-333G>C		intron_variant	Intron 1 of 3	4		ENSP00000432936.1
FCMR	ENST00000529560.1	c.-36-388G>C		intron_variant	Intron 1 of 3	4		ENSP00000437331.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59742 AN: 151874 Hom.: 12289 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.393 AC: 59777 AN: 151992 Hom.: 12301 Cov.: 32 AF XY: 0.386 AC XY: 28696 AN XY: 74284

African (AFR) AF: 0.291 AC: 12075 AN: 41436

American (AMR) AF: 0.354 AC: 5409 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1742 AN: 5156

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4816

European-Finnish (FIN) AF: 0.408 AC: 4311 AN: 10560

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31890 AN: 67960

Other (OTH) AF: 0.441 AC: 931 AN: 2112

Alfa AF: 0.290 Hom.: 731

Bravo AF: 0.386

Asia WGS AF: 0.283 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.34
PhyloP100		-2.1
PromoterAI		-0.0052	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs291084; hg19: chr1-207095623;