18-13681902-G-T

Variant names:

• chr18-13681902-G-T
• rs148603152
• NM_152352.4:c.176C>A

Variant summary

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

The NM_152352.4(FAM210A):​c.176C>A​(p.Ser59Tyr) 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. 14/22 in silico tools predict 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. S59C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM210A NM_152352.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.53
• Publications: 3 publications found

Genes affected

FAM210A (HGNC:28346): (family with sequence similarity 210 member A) Predicted to be located in cytoplasm. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

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=0.16541305).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152352.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM210A	NM_152352.4	MANE Select	c.176C>A	p.Ser59Tyr	missense	Exon 2 of 4	NP_689565.2	Q96ND0
	FAM210A	NM_001098801.2		c.176C>A	p.Ser59Tyr	missense	Exon 3 of 5	NP_001092271.1	Q96ND0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM210A	ENST00000651643.1	MANE Select	c.176C>A	p.Ser59Tyr	missense	Exon 2 of 4	ENSP00000498370.1	Q96ND0
	FAM210A	ENST00000585785.1	TSL:1	n.265-15189C>A		intron	N/A
	FAM210A	ENST00000322247.7	TSL:2	c.176C>A	p.Ser59Tyr	missense	Exon 3 of 5	ENSP00000323635.3	Q96ND0

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.076	T
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.35
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.70	T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.8	L
PhyloP100		4.5
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.78	N
REVEL	Benign	0.10
Sift	Uncertain	0.022	D
Sift4G	Uncertain	0.038	D
Polyphen		0.41	B
Vest4		0.38
MutPred		0.34		Loss of disorder (P = 0.0289)
MVP		0.34
MPC		0.35
ClinPred		0.36	T
GERP RS		3.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.047
gMVP		0.45
Mutation Taster		=93/7	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: rs148603152; hg19: chr18-13681901;