11-65641237-G-A

Variant names:

• chr11-65641237-G-A
• rs3741379
• NM_006747.4:c.316G>A

Variant summary

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

The NM_006747.4(SIPA1):​c.316G>A​(p.Ala106Thr) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A106S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SIPA1 NM_006747.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 0 publications found

Genes affected

SIPA1 (HGNC:10885): (signal-induced proliferation-associated 1) The product of this gene is a mitogen induced GTPase activating protein (GAP). It exhibits a specific GAP activity for Ras-related regulatory proteins Rap1 and Rap2, but not for Ran or other small GTPases. This protein may also hamper mitogen-induced cell cycle progression when abnormally or prematurely expressed. It is localized to the perinuclear region. Two alternatively spliced variants encoding the same isoform have been characterized to date. [provided by RefSeq, Jul 2008]

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=0.03077069).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIPA1	NM_006747.4	c.316G>A	p.Ala106Thr	missense_variant	Exon 2 of 16	ENST00000534313.6	NP_006738.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIPA1	ENST00000534313.6	c.316G>A	p.Ala106Thr	missense_variant	Exon 2 of 16	1	NM_006747.4	ENSP00000436269.1
SIPA1	ENST00000394224.4	c.316G>A	p.Ala106Thr	missense_variant	Exon 2 of 16	1		ENSP00000377771.3
SIPA1	ENST00000527525.5	c.316G>A	p.Ala106Thr	missense_variant	Exon 2 of 17	2		ENSP00000433686.1
SIPA1	ENST00000533361.1	c.*8G>A		downstream_gene_variant		4		ENSP00000436683.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.4
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T;T;T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.035	N
LIST_S2	Benign	0.64	.;T;T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.031	T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.49	N;.;N
PhyloP100		-0.31
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.99	N;N;N
REVEL	Benign	0.20
Sift	Benign	0.62	T;T;T
Sift4G	Benign	0.41	T;T;T
Polyphen		0.0	B;B;B
Vest4		0.035
MutPred		0.20		Gain of glycosylation at A106 (P = 2e-04);Gain of glycosylation at A106 (P = 2e-04);Gain of glycosylation at A106 (P = 2e-04);
MVP		0.37
MPC		0.59
ClinPred		0.066	T
GERP RS		-5.2
Varity_R		0.055
gMVP		0.18
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

Other links and lift over

dbSNP: rs3741379; hg19: chr11-65408708; COSMIC: COSV63134444; COSMIC: COSV63134444;