chr1-197101675-T-C

Variant names:

• chr1-197101675-T-C
• rs587783267
• NM_018136.5:c.7576A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_018136.5(ASPM):​c.7576A>G​(p.Asn2526Asp) 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. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. N2526N) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ASPM NM_018136.5 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0920
• Publications: 1 publications found

Genes affected

ASPM (HGNC:19048): (assembly factor for spindle microtubules) This gene is the human ortholog of the Drosophila melanogaster 'abnormal spindle' gene (asp), which is essential for normal mitotic spindle function in embryonic neuroblasts. Studies in mouse also suggest a role of this gene in mitotic spindle regulation, with a preferential role in regulating neurogenesis. Mutations in this gene are associated with microcephaly primary type 5. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

ASPM Gene-Disease associations (from GenCC):

• microcephaly 5, primary, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• autosomal recessive primary microcephaly

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen

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=0.09998092).
• BP6: Variant 1-197101675-T-C is Benign according to our data. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197101675-T-C is described in CliVar as Benign. Clinvar id is 157872.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASPM	NM_018136.5	c.7576A>G	p.Asn2526Asp	missense_variant	Exon 18 of 28	ENST00000367409.9	NP_060606.3
ASPM	NM_001206846.2	c.4066-5511A>G		intron_variant	Intron 17 of 26		NP_001193775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASPM	ENST00000367409.9	c.7576A>G	p.Asn2526Asp	missense_variant	Exon 18 of 28	1	NM_018136.5	ENSP00000356379.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 61

GnomAD4 genome Cov.: 33

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	2.1
DANN	Benign	0.72
DEOGEN2	Benign	0.032	T
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.025	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.72	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.092
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.098
Sift	Benign	0.51	T
Sift4G	Benign	0.50	T
Polyphen		0.047	B
Vest4		0.14
MutPred		0.45		Loss of MoRF binding (P = 0.0931);
MVP		0.56
ClinPred		0.13	T
GERP RS		-1.2
Varity_R		0.049
gMVP		0.022
Mutation Taster		=96/4	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: rs587783267; hg19: chr1-197070805;