chr1-206961094-G-C

Variant names:

• chr1-206961094-G-C
• rs1453504402
• NM_001170631.2:c.782C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001170631.2(FCAMR):​c.782C>G​(p.Ala261Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000714 in 1,399,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A261V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000071 (0 hom.)
• Consequence: FCAMR NM_001170631.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 0 publications found

Genes affected

FCAMR (HGNC:24692): (Fc alpha and mu receptor) Predicted to enable IgA binding activity; IgM binding activity; and transmembrane signaling receptor activity. Predicted to be involved in adaptive immune response. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.028388172).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCAMR	NM_001170631.2	c.782C>G	p.Ala261Gly	missense_variant	Exon 6 of 8	ENST00000324852.9	NP_001164102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCAMR	ENST00000324852.9	c.782C>G	p.Ala261Gly	missense_variant	Exon 6 of 8	2	NM_001170631.2	ENSP00000316491.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000714 AC: 10 AN: 1399592 Hom.: 0 Cov.: 31 AF XY: 0.00000290 AC XY: 2 AN XY: 690286

African (AFR) AF: 0.00 AC: 0 AN: 31598

American (AMR) AF: 0.00 AC: 0 AN: 35708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25182

East Asian (EAS) AF: 0.00 AC: 0 AN: 35738

South Asian (SAS) AF: 0.00 AC: 0 AN: 79236

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5700

European-Non Finnish (NFE) AF: 0.00000927 AC: 10 AN: 1079018

Other (OTH) AF: 0.00 AC: 0 AN: 58052

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.061
DANN	Benign	0.61
DEOGEN2	Benign	0.0025	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.031	N
LIST_S2	Benign	0.34	T
M_CAP	Benign	0.0048	T
MetaRNN	Benign	0.028	T
MetaSVM	Benign	-0.91	T
PhyloP100		-0.58
PrimateAI	Benign	0.21	T
PROVEAN	Benign	0.69	N
REVEL	Benign	0.010
Sift	Benign	0.77	T
Sift4G	Benign	0.73	T
Vest4		0.016
MVP		0.067
MPC		0.16
ClinPred		0.048	T
GERP RS		-1.4
gMVP		0.39
Mutation Taster		=97/3	polymorphism

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: rs1453504402; hg19: chr1-207134439;