chr1-206963993-G-A

Variant names:

• chr1-206963993-G-A
• rs2000059
• NM_001170631.2:c.314-1442C>T

Variant summary

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

The NM_001170631.2(FCAMR):​c.314-1442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 152,242 control chromosomes in the GnomAD database, including 569 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 0.072 (569 hom., cov: 32)
• Consequence: FCAMR NM_001170631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001170631.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCAMR	NM_001170631.2	MANE Select	c.314-1442C>T		intron	N/A	NP_001164102.1
	FCAMR	NM_001424868.1		c.179-1442C>T		intron	N/A	NP_001411797.1
	FCAMR	NM_001122979.3		c.314-1442C>T		intron	N/A	NP_001116451.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCAMR	ENST00000324852.9	TSL:2 MANE Select	c.314-1442C>T		intron	N/A	ENSP00000316491.4
	FCAMR	ENST00000450945.3	TSL:1	c.314-1442C>T		intron	N/A	ENSP00000392707.2
	FCAMR	ENST00000400962.8	TSL:5	c.314-1442C>T		intron	N/A	ENSP00000383746.3

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10997 AN: 152124 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0722 AC: 10998 AN: 152242 Hom.: 569 Cov.: 32 AF XY: 0.0698 AC XY: 5193 AN XY: 74432

African (AFR) AF: 0.0283 AC: 1175 AN: 41546

American (AMR) AF: 0.0501 AC: 767 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3466

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4828

European-Finnish (FIN) AF: 0.113 AC: 1194 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7456 AN: 68010

Other (OTH) AF: 0.0567 AC: 120 AN: 2116

Alfa AF: 0.0927 Hom.: 1393

Bravo AF: 0.0651

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.37
PhyloP100		0.65
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: rs2000059; hg19: chr1-207137338;