rs1241100293

Variant names:

• chr7-103086667-C-A
• rs1241100293
• NM_031905.5:c.431C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-103086667-C-A
• chr7-103086667-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_031905.5(ARMC10):​c.431C>A​(p.Ala144Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. A144G) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ARMC10 NM_031905.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 0 publications found

Genes affected

ARMC10 (HGNC:21706): (armadillo repeat containing 10) This gene encodes a protein that contains an armadillo repeat and transmembrane domain. The encoded protein decreases the transcriptional activity of the tumor suppressor protein p53 through direct interaction with the DNA-binding domain of p53, and may play a role in cell growth and survival. Upregulation of this gene may play a role in hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 3. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMC10	NM_031905.5	c.431C>A	p.Ala144Glu	missense_variant	Exon 4 of 7	ENST00000323716.8	NP_114111.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMC10	ENST00000323716.8	c.431C>A	p.Ala144Glu	missense_variant	Exon 4 of 7	1	NM_031905.5	ENSP00000319412.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00 AC: 0 AN: 228948 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Benign	-0.078	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	21
DANN	Benign	0.93
DEOGEN2	Benign	0.013	.;.;.;.;.;T;T;T
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.35
FATHMM_MKL	Benign	0.62	D
LIST_S2	Uncertain	0.89	D;T;D;D;D;D;D;.
M_CAP	Benign	0.027	D
MetaRNN	Uncertain	0.51	D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	-0.16	.;.;N;.;.;N;.;.
PhyloP100		2.0
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-3.0	D;N;D;N;N;N;D;N
REVEL	Benign	0.21
Sift	Benign	0.094	T;T;D;T;D;T;D;T
Sift4G	Uncertain	0.0040	D;T;D;T;D;T;D;T
Polyphen		0.37, 0.49, 0.18, 0.63, 0.60	.;.;B;P;B;P;P;.
Vest4		0.40
MutPred		0.81		.;.;Gain of disorder (P = 0.0467);.;.;Gain of disorder (P = 0.0467);.;.;
MVP		0.44
MPC		0.17
ClinPred		0.83	D
GERP RS		3.6
PromoterAI		-0.0042	Neutral
Varity_R		0.28
gMVP		0.58
Mutation Taster		=83/17	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: rs1241100293; hg19: chr7-102727114;