rs1856746

Positions:

• chr1-206970077-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170631.2(FCAMR):​c.39+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,613,194 control chromosomes in the GnomAD database, including 186,225 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 0.57 (27048 hom., cov: 31)
  • Exomes 𝑓: 0.46 (159177 hom.)
• Consequence: FCAMR NM_001170631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCAMR	NM_001170631.2	c.39+10T>C		intron_variant		ENST00000324852.9	NP_001164102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCAMR	ENST00000324852.9	c.39+10T>C		intron_variant		2	NM_001170631.2	ENSP00000316491	A2
FCAMR	ENST00000450945.3	c.39+10T>C		intron_variant		1		ENSP00000392707	P2
FCAMR	ENST00000400962.8	c.39+10T>C		intron_variant		5		ENSP00000383746	P2
FCAMR	ENST00000324863.6	c.39+10T>C		intron_variant, NMD_transcript_variant		5		ENSP00000317155

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86227 AN: 151900 Hom.: 26984 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.580

GnomAD3 exomes AF: 0.471 AC: 117049 AN: 248744 Hom.: 29568 AF XY: 0.457 AC XY: 61802 AN XY: 135196

Gnomad AFR exome AF: 0.866

Gnomad AMR exome AF: 0.512

Gnomad ASJ exome AF: 0.567

Gnomad EAS exome AF: 0.433

Gnomad SAS exome AF: 0.295

Gnomad FIN exome AF: 0.390

Gnomad NFE exome AF: 0.464

Gnomad OTH exome AF: 0.475

GnomAD4 exome AF: 0.459 AC: 671024 AN: 1461178 Hom.: 159177 Cov.: 39 AF XY: 0.454 AC XY: 330023 AN XY: 726946

Gnomad4 AFR exome AF: 0.873

Gnomad4 AMR exome AF: 0.510

Gnomad4 ASJ exome AF: 0.562

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.297

Gnomad4 FIN exome AF: 0.396

Gnomad4 NFE exome AF: 0.457

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.568 AC: 86350 AN: 152016 Hom.: 27048 Cov.: 31 AF XY: 0.558 AC XY: 41467 AN XY: 74298

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.584

Alfa AF: 0.497 Hom.: 28906

Bravo AF: 0.593

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1856746; hg19: chr1-207143422; COSMIC: COSV61367093;