NM_152347.5:c.406C>G

Variant names:

• chr17-47344264-C-G
• rs755943359
• NM_152347.5:c.406C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152347.5(EFCAB13):​c.406C>G​(p.Pro136Ala) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EFCAB13 NM_152347.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

Genes affected

EFCAB13 (HGNC:26864): (EF-hand calcium binding domain 13)

ENSG00000259753 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14315486).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB13	NM_152347.5	c.406C>G	p.Pro136Ala	missense_variant	Exon 7 of 25	ENST00000331493.7	NP_689560.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB13	ENST00000331493.7	c.406C>G	p.Pro136Ala	missense_variant	Exon 7 of 25	1	NM_152347.5	ENSP00000332111.2
ENSG00000259753	ENST00000560629.1	n.*395C>G		non_coding_transcript_exon_variant	Exon 18 of 18	2		ENSP00000456711.2
ENSG00000259753	ENST00000560629.1	n.*395C>G		3_prime_UTR_variant	Exon 18 of 18	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	13
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0032	T;.
Eigen	Benign	-0.44
Eigen_PC	Benign	-0.68
FATHMM_MKL	Benign	0.027	N
LIST_S2	Benign	0.47	T;T
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	0.90	L;L
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-1.3	N;N
REVEL	Benign	0.075
Sift	Pathogenic	0.0	D;D
Sift4G	Benign	0.17	T;T
Polyphen		0.97	D;.
Vest4		0.32
MutPred		0.20		Loss of loop (P = 0.0288);Loss of loop (P = 0.0288);
MVP		0.099
MPC		0.32
ClinPred		0.23	T
GERP RS		-0.0052
Varity_R		0.058
gMVP		0.019

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

Publications

LitVar

Other links and lift over

dbSNP: rs755943359; hg19: chr17-45421630;