rs2000059

Positions:

• chr1-206963993-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCAMR	NM_001170631.2	c.314-1442C>T		intron_variant		ENST00000324852.9	NP_001164102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCAMR	ENST00000324852.9	c.314-1442C>T		intron_variant		2	NM_001170631.2	ENSP00000316491	A2
FCAMR	ENST00000450945.3	c.314-1442C>T		intron_variant		1		ENSP00000392707	P2
FCAMR	ENST00000400962.8	c.314-1442C>T		intron_variant		5		ENSP00000383746	P2
FCAMR	ENST00000324863.6	c.*293-1442C>T		intron_variant, NMD_transcript_variant		5		ENSP00000317155

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

Gnomad4 AFR AF: 0.0283

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0567

Alfa AF: 0.0966 Hom.: 1117

Bravo AF: 0.0651

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.37

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: rs2000059; hg19: chr1-207137338;