10-59264163-A-C

Variant names:

• chr10-59264163-A-C
• NM_198215.4:c.946T>G

Variant summary

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

The NM_198215.4(FAM13C):​c.946T>G​(p.Ser316Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: FAM13C NM_198215.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.07

Genes affected

FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

ACMG classification

Verdict is Uncertain_significance. Variant got 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
FAM13C	NM_198215.4	c.946T>G	p.Ser316Ala	missense_variant	Exon 9 of 14	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.946T>G	p.Ser316Ala	missense_variant	Exon 9 of 14	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 05, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.946T>G (p.S316A) alteration is located in exon 9 (coding exon 9) of the FAM13C gene. This alteration results from a T to G substitution at nucleotide position 946, causing the serine (S) at amino acid position 316 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Uncertain	0.044	T
BayesDel_noAF	Benign	-0.17
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.22	T;.;.;.;.;.;.;.
Eigen	Uncertain	0.29
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.71	T;T;T;T;T;T;T;T
M_CAP	Uncertain	0.11	D
MetaRNN	Uncertain	0.44	T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.026	D
MutationAssessor	Uncertain	2.6	M;.;.;.;.;.;M;.
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-2.4	.;.;.;.;N;N;N;D
REVEL	Uncertain	0.47
Sift	Benign	0.040	.;.;.;.;D;D;D;T
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D
Polyphen		0.78	P;.;.;.;.;B;B;.
Vest4		0.32
MutPred		0.20		Loss of phosphorylation at S316 (P = 0.005);.;.;.;.;Loss of phosphorylation at S316 (P = 0.005);Loss of phosphorylation at S316 (P = 0.005);.;
MVP		0.80
ClinPred		0.87	D
GERP RS		5.8
Varity_R		0.28
gMVP		0.51

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-61023923;