Genetic Variant SLAMF1:c.957+30G>C (chr1-160612458-C-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_003037.5(SLAMF1):c.957+30G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 1,445,430 control chromosomes in the GnomAD database, including 146,030 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 0.37 ( 12140 hom., cov: 29)

Exomes 𝑓: 0.45 ( 133890 hom. )

Consequence

SLAMF1
NM_003037.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0560

Publications

7 publications found

Variant links:

Genes affected

SLAMF1 (HGNC:10903): (signaling lymphocytic activation molecule family member 1) Enables SH2 domain binding activity and identical protein binding activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SLAMF1 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5 link	c.957+30G>C		intron_variant	Intron 6 of 6	ENST00000302035.11	NP_003028.1	Q13291-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLAMF1	ENST00000302035.11 link	c.957+30G>C		intron_variant	Intron 6 of 6	1	NM_003037.5	ENSP00000306190.6		Q13291-1
SLAMF1	ENST00000538290.2 link	c.1040+30G>C		intron_variant	Intron 7 of 7	1		ENSP00000438406.2		Q13291-4

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55468

AN:

151638

Hom.:

12133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.362

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.353

GnomAD2 exomes

AF:

0.451

AC:

105249

AN:

233262

AF XY:

0.460

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.380

Gnomad ASJ exome

AF:

0.439

Gnomad EAS exome

AF:

0.683

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.452

Gnomad OTH exome

AF:

0.435

GnomAD4 exome

AF:

0.449

AC:

580548

AN:

1293674

Hom.:

133890

Cov.:

AF XY:

0.452

AC XY:

294063

AN XY:

650840

show subpopulations

African (AFR)

AF:

0.114

AC:

3374

AN:

29676

American (AMR)

AF:

0.378

AC:

16029

AN:

42446

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

10877

AN:

24744

East Asian (EAS)

AF:

0.605

AC:

23458

AN:

38774

South Asian (SAS)

AF:

0.514

AC:

41569

AN:

80938

European-Finnish (FIN)

AF:

0.531

AC:

28059

AN:

52796

Middle Eastern (MID)

AF:

0.317

AC:

1709

AN:

5398

European-Non Finnish (NFE)

AF:

0.448

AC:

431528

AN:

964096

Other (OTH)

AF:

0.437

AC:

23945

AN:

54806

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

14866

29732

44599

59465

74331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12252

24504

36756

49008

61260

<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:

0.366

AC:

55496

AN:

151756

Hom.:

12140

Cov.:

AF XY:

0.374

AC XY:

27734

AN XY:

74108

show subpopulations

African (AFR)

AF:

0.122

AC:

5064

AN:

41396

American (AMR)

AF:

0.362

AC:

5520

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.426

AC:

1476

AN:

3468

East Asian (EAS)

AF:

0.666

AC:

3417

AN:

5130

South Asian (SAS)

AF:

0.525

AC:

2517

AN:

4794

European-Finnish (FIN)

AF:

0.528

AC:

5532

AN:

10482

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.451

AC:

30615

AN:

67914

Other (OTH)

AF:

0.358

AC:

754

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1594

3189

4783

6378

7972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.403

Hom.:

2494

Bravo

AF:

0.341

Asia WGS

AF:

0.533

AC:

1853

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.5

(source)

DANN

Benign

0.62

PhyloP100

-0.056

Mutation Taster

=64/36

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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