dbSNP rs1856746: FCAMR:c.39+10T>C (chr1-206970077-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

27 publications found

Variant links:

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]

FCAMR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCAMR	NM_001170631.2 link	c.39+10T>C		intron_variant	Intron 1 of 7	ENST00000324852.9	NP_001164102.1	A0A0B4J1S2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FCAMR	ENST00000324852.9 link	c.39+10T>C	intron_variant	Intron 1 of 7	2	NM_001170631.2	ENSP00000316491.4	A0A0B4J1S2
FCAMR	ENST00000450945.3 link	c.39+10T>C	intron_variant	Intron 2 of 7	1		ENSP00000392707.2	Q8WWV6
FCAMR	ENST00000400962.8 link	c.39+10T>C	intron_variant	Intron 1 of 6	5		ENSP00000383746.3	Q8WWV6
FCAMR	ENST00000324863.6 link	n.39+10T>C	intron_variant	Intron 1 of 8	5		ENSP00000317155.2	F8W7R9

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86227

AN:

151900

Hom.:

26984

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.471

AC:

117049

AN:

248744

AF XY:

0.457

show subpopulations

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 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.:

AF XY:

0.454

AC XY:

330023

AN XY:

726946

show subpopulations

African (AFR)

AF:

0.873

AC:

29207

AN:

33450

American (AMR)

AF:

0.510

AC:

22811

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

14678

AN:

26118

East Asian (EAS)

AF:

0.429

AC:

16999

AN:

39664

South Asian (SAS)

AF:

0.297

AC:

25581

AN:

86232

European-Finnish (FIN)

AF:

0.396

AC:

21163

AN:

53406

Middle Eastern (MID)

AF:

0.564

AC:

3255

AN:

5768

European-Non Finnish (NFE)

AF:

0.457

AC:

507941

AN:

1111502

Other (OTH)

AF:

0.487

AC:

29389

AN:

60354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

16842

33684

50526

67368

84210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15220

30440

45660

60880

76100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.568

AC:

86350

AN:

152016

Hom.:

27048

Cov.:

AF XY:

0.558

AC XY:

41467

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.855

AC:

35472

AN:

41498

American (AMR)

AF:

0.525

AC:

8021

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.554

AC:

1920

AN:

3466

East Asian (EAS)

AF:

0.447

AC:

2302

AN:

5148

South Asian (SAS)

AF:

0.272

AC:

1312

AN:

4820

European-Finnish (FIN)

AF:

0.381

AC:

4028

AN:

10574

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.463

AC:

31436

AN:

67914

Other (OTH)

AF:

0.584

AC:

1231

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1703

3405

5108

6810

8513

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.505

Hom.:

37304

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

(source)

DANN

Benign

0.62

PhyloP100

-1.4

PromoterAI

0.052

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over