chr10-114447901-G-C

Variant names:

• chr10-114447901-G-C
• rs1224696934
• NM_002313.7:c.1714C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002313.7(ABLIM1):​c.1714C>G​(p.Pro572Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. P572S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ABLIM1 NM_002313.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.74
• Publications: 1 publications found

Genes affected

ABLIM1 (HGNC:78): (actin binding LIM protein 1) This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2017]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24286312).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.1714C>G	p.Pro572Ala	missense_variant	Exon 15 of 23	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.1714C>G	p.Pro572Ala	missense_variant	Exon 15 of 23	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000207 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	0.0028	T
BayesDel_noAF	Benign	-0.23
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	.;.;.;T;.;T;.;T;.
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.81	T;D;D;D;T;T;D;D;D
M_CAP	Benign	0.0096	T
MetaRNN	Benign	0.24	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.6	.;.;.;.;.;.;.;M;.
PhyloP100		4.7
PrimateAI	Benign	0.46	T
PROVEAN	Uncertain	-3.3	D;.;N;.;.;.;.;.;.
REVEL	Benign	0.20
Sift	Uncertain	0.012	D;.;T;.;.;.;.;.;.
Sift4G	Benign	0.070	T;T;T;T;T;T;T;T;.
Polyphen		0.0010	B;.;B;.;B;.;.;B;.
Vest4		0.43
MutPred		0.29		.;.;.;.;.;.;.;Gain of loop (P = 0.024);.;
MVP		0.34
MPC		0.37
ClinPred		0.76	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.065
gMVP		0.54
Mutation Taster		=66/34	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1224696934; hg19: chr10-116207660;