Genetic Variant NM_003037.5: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

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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