Variant rs12076998 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003037.5(SLAMF1):c.-33C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 1,227,172 control chromosomes in the GnomAD database, including 2,883 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 0.071 ( 427 hom., cov: 31)

Exomes 𝑓: 0.064 ( 2456 hom. )

Consequence

SLAMF1
NM_003037.5 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

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:

SLAMF1 (HGNC:):

SLAMF1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLAMF1	NM_003037.5 linkuse as main transcript	c.-33C>T		5_prime_UTR_premature_start_codon_gain_variant	1/7	ENST00000302035.11	NP_003028.1	Q13291-1
SLAMF1	NM_003037.5 linkuse as main transcript	c.-33C>T		5_prime_UTR_variant	1/7	ENST00000302035.11	NP_003028.1	Q13291-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLAMF1	ENST00000302035.11 linkuse as main transcript	c.-33C>T	5_prime_UTR_premature_start_codon_gain_variant	1/7	1	NM_003037.5	ENSP00000306190.6	Q13291-1
SLAMF1	ENST00000302035.11 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/7	1	NM_003037.5	ENSP00000306190.6	Q13291-1
SLAMF1	ENST00000494463.1 linkuse as main transcript	n.44C>T	non_coding_transcript_exon_variant	1/2	1
SLAMF1	ENST00000538290.2 linkuse as main transcript	c.-33C>T	upstream_gene_variant		1		ENSP00000438406.2	Q13291-4

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10720

AN:

152024

Hom.:

424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0485

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0540

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0696

Gnomad OTH

AF:

0.0632

GnomAD3 exomes

AF:

0.0560

AC:

12415

AN:

221768

Hom.:

429

AF XY:

0.0552

AC XY:

6609

AN XY:

119706

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.0400

Gnomad ASJ exome

AF:

0.0228

Gnomad EAS exome

AF:

0.00392

Gnomad SAS exome

AF:

0.0320

Gnomad FIN exome

AF:

0.0594

Gnomad NFE exome

AF:

0.0720

Gnomad OTH exome

AF:

0.0610

GnomAD4 exome

AF:

0.0635

AC:

68309

AN:

1075030

Hom.:

2456

Cov.:

AF XY:

0.0623

AC XY:

34277

AN XY:

550210

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.0410

Gnomad4 ASJ exome

AF:

0.0234

Gnomad4 EAS exome

AF:

0.00307

Gnomad4 SAS exome

AF:

0.0327

Gnomad4 FIN exome

AF:

0.0614

Gnomad4 NFE exome

AF:

0.0711

Gnomad4 OTH exome

AF:

0.0605

GnomAD4 genome

AF:

0.0706

AC:

10739

AN:

152142

Hom.:

427

Cov.:

AF XY:

0.0687

AC XY:

5112

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.103

Gnomad4 AMR

AF:

0.0483

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.00290

Gnomad4 SAS

AF:

0.0268

Gnomad4 FIN

AF:

0.0540

Gnomad4 NFE

AF:

0.0696

Gnomad4 OTH

AF:

0.0625

Alfa

AF:

0.0647

Hom.:

Bravo

AF:

0.0723

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over