1-160646915-A-G

Variant names:

• chr1-160646915-A-G
• NM_003037.5:c.31T>C
• SLAMF1 p.Phe11Leu

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003037.5(SLAMF1):​c.31T>C​(p.Phe11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLAMF1 NM_003037.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• Publications: 0 publications found

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]

ENSG00000228863 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.055961937).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	NM_003037.5	MANE Select	c.31T>C	p.Phe11Leu	missense	Exon 1 of 7	NP_003028.1	Q13291-1
	SLAMF1	NM_001330754.2		c.31T>C	p.Phe11Leu	missense	Exon 1 of 8	NP_001317683.1	Q13291-4
	SLAMF1	NR_104399.3		n.130T>C		non_coding_transcript_exon	Exon 1 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLAMF1	ENST00000302035.11	TSL:1 MANE Select	c.31T>C	p.Phe11Leu	missense	Exon 1 of 7	ENSP00000306190.6	Q13291-1
	SLAMF1	ENST00000538290.2	TSL:1	c.31T>C	p.Phe11Leu	missense	Exon 1 of 8	ENSP00000438406.2	Q13291-4
	SLAMF1	ENST00000494463.1	TSL:1	n.107T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.15
DANN	Benign	0.51
DEOGEN2	Benign	0.042	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0083	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.0026	T
MetaRNN	Benign	0.056	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.12	N
PhyloP100		-0.80
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.36	N
REVEL	Benign	0.020
Sift	Benign	0.67	T
Sift4G	Benign	0.78	T
PromoterAI		-0.13	Neutral
Varity_R		0.025
gMVP		0.39
Mutation Taster		=97/3	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-160616705;