Genetic Variant SLAMF1:c.*523T>C (chr1-160610225-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_001330754.2(SLAMF1):c.*540T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 447,572 control chromosomes in the GnomAD database, including 68,560 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 0.48 ( 20046 hom., cov: 32)

Exomes 𝑓: 0.56 ( 48514 hom. )

Consequence

SLAMF1
NM_001330754.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

Publications

19 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:

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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 (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330754.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLAMF1	NM_003037.5	MANE Select	c.*523T>C	3_prime_UTR	Exon 7 of 7	NP_003028.1
SLAMF1	NM_001330754.2		c.*540T>C	3_prime_UTR	Exon 8 of 8	NP_001317683.1
SLAMF1	NR_104399.3		n.1556T>C	non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLAMF1	ENST00000302035.11	TSL:1 MANE Select	c.*523T>C	3_prime_UTR	Exon 7 of 7	ENSP00000306190.6
SLAMF1	ENST00000878659.1		c.*523T>C	3_prime_UTR	Exon 6 of 6	ENSP00000548717.1
SLAMF1	ENST00000878657.1		c.*523T>C	3_prime_UTR	Exon 6 of 6	ENSP00000548716.1

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73701

AN:

151974

Hom.:

20035

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.459

Gnomad ASJ

AF:

0.562

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.549

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.466

GnomAD4 exome

AF:

0.565

AC:

166883

AN:

295480

Hom.:

48514

Cov.:

AF XY:

0.564

AC XY:

94914

AN XY:

168420

show subpopulations

African (AFR)

AF:

0.223

AC:

1806

AN:

8104

American (AMR)

AF:

0.461

AC:

11595

AN:

25170

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

5929

AN:

10422

East Asian (EAS)

AF:

0.683

AC:

6191

AN:

9070

South Asian (SAS)

AF:

0.539

AC:

31233

AN:

57930

European-Finnish (FIN)

AF:

0.695

AC:

8803

AN:

12658

Middle Eastern (MID)

AF:

0.406

AC:

1111

AN:

2734

European-Non Finnish (NFE)

AF:

0.596

AC:

92659

AN:

155568

Other (OTH)

AF:

0.547

AC:

7556

AN:

13824

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3320

6640

9959

13279

16599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.485

AC:

73735

AN:

152092

Hom.:

20046

Cov.:

AF XY:

0.490

AC XY:

36429

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.229

AC:

9503

AN:

41498

American (AMR)

AF:

0.459

AC:

7007

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

1950

AN:

3472

East Asian (EAS)

AF:

0.681

AC:

3528

AN:

5182

South Asian (SAS)

AF:

0.550

AC:

2648

AN:

4814

European-Finnish (FIN)

AF:

0.682

AC:

7203

AN:

10566

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.591

AC:

40180

AN:

67964

Other (OTH)

AF:

0.471

AC:

994

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1739

3478

5218

6957

8696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.547

Hom.:

71436

Bravo

AF:

0.458

Asia WGS

AF:

0.557

AC:

1935

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.5

(source)

DANN

Benign

0.58

PhyloP100

-0.015

Mutation Taster

=100/0

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over