dbSNP rs2025515: SLAMF1:c.957+65G>T (chr1-160612423-C-A) – 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+65G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,006,452 control chromosomes in the GnomAD database, including 67,852 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 0.36 ( 11844 hom., cov: 28)

Exomes 𝑓: 0.41 ( 56008 hom. )

Consequence

SLAMF1
NM_003037.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

Publications

3 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5 link	c.957+65G>T		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+65G>T		intron_variant	Intron 6 of 6	1	NM_003037.5	ENSP00000306190.6		Q13291-1
SLAMF1	ENST00000538290.2 link	c.1040+65G>T		intron_variant	Intron 7 of 7	1		ENSP00000438406.2		Q13291-4

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

54857

AN:

150690

Hom.:

11841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.663

Gnomad SAS

AF:

0.522

Gnomad FIN

AF:

0.517

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.411

AC:

351735

AN:

855656

Hom.:

56008

AF XY:

0.412

AC XY:

179924

AN XY:

436532

show subpopulations

African (AFR)

AF:

0.113

AC:

2217

AN:

19574

American (AMR)

AF:

0.336

AC:

8037

AN:

23924

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

7367

AN:

18600

East Asian (EAS)

AF:

0.522

AC:

16715

AN:

32034

South Asian (SAS)

AF:

0.444

AC:

26593

AN:

59910

European-Finnish (FIN)

AF:

0.471

AC:

21051

AN:

44662

Middle Eastern (MID)

AF:

0.293

AC:

1258

AN:

4290

European-Non Finnish (NFE)

AF:

0.412

AC:

253245

AN:

613956

Other (OTH)

AF:

0.394

AC:

15252

AN:

38706

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

8681

17361

26042

34722

43403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6758

13516

20274

27032

33790

<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:

0.364

AC:

54877

AN:

150796

Hom.:

11844

Cov.:

AF XY:

0.372

AC XY:

27390

AN XY:

73582

show subpopulations

African (AFR)

AF:

0.122

AC:

5033

AN:

41182

American (AMR)

AF:

0.361

AC:

5474

AN:

15164

Ashkenazi Jewish (ASJ)

AF:

0.424

AC:

1468

AN:

3462

East Asian (EAS)

AF:

0.664

AC:

3381

AN:

5092

South Asian (SAS)

AF:

0.524

AC:

2494

AN:

4764

European-Finnish (FIN)

AF:

0.517

AC:

5282

AN:

10210

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.450

AC:

30403

AN:

67622

Other (OTH)

AF:

0.354

AC:

742

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1534

3069

4603

6138

7672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.316

Hom.:

3142

Bravo

AF:

0.341

Asia WGS

AF:

0.517

AC:

1797

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.13

(source)

DANN

Benign

0.24

PhyloP100

-1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over