12-100942462-C-T

Variant names:

• chr12-100942462-C-T
• rs199936621
• NM_001286615.2:c.383C>T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP2

The NM_001286615.2(ANO4):​c.383C>T​(p.Ser128Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. S128Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANO4 NM_001286615.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.01
• Publications: 3 publications found

Genes affected

ANO4 (HGNC:23837): (anoctamin 4) Enables intracellular calcium activated chloride channel activity. Involved in chloride transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ANO4 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 7 curated pathogenic missense variants (we use a threshold of 10). The gene has 1 curated benign missense variants. Gene score misZ: 2.5332 (below the threshold of 3.09). Trascript score misZ: 3.1552 (above the threshold of 3.09). GenCC associations: The gene is linked to complex neurodevelopmental disorder.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO4	NM_001286615.2	c.383C>T	p.Ser128Phe	missense_variant	Exon 5 of 28	ENST00000392977.8	NP_001273544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO4	ENST00000392977.8	c.383C>T	p.Ser128Phe	missense_variant	Exon 5 of 28	2	NM_001286615.2	ENSP00000376703.3
ANO4	ENST00000644049.1	c.881C>T	p.Ser294Phe	missense_variant	Exon 7 of 30			ENSP00000494481.1
ANO4	ENST00000392979.7	c.278C>T	p.Ser93Phe	missense_variant	Exon 4 of 27	2		ENSP00000376705.3
ANO4	ENST00000549155.6	n.881C>T		non_coding_transcript_exon_variant	Exon 7 of 11	2		ENSP00000449116.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.29	.;.;T
Eigen	Uncertain	0.62
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	D;D;D
M_CAP	Benign	0.034	D
MetaRNN	Uncertain	0.46	T;T;T
MetaSVM	Benign	-0.36	T
MutationAssessor	Benign	1.6	.;.;L
PhyloP100		7.0
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-3.1	.;D;D
REVEL	Benign	0.26
Sift	Uncertain	0.013	.;D;D
Sift4G	Uncertain	0.025	.;D;D
Polyphen		0.92, 0.83	.;P;P
Vest4		0.41, 0.41
MutPred		0.36		.;.;Loss of disorder (P = 0.0393);
MVP		0.068
MPC		1.4
ClinPred		0.98	D
GERP RS		5.6
Varity_R		0.25
gMVP		0.28
Mutation Taster		=48/52	disease causing

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: rs199936621; hg19: chr12-101336240; COSMIC: COSV100152378;