rs766444513

Variant names:

• chr7-102749382-C-A
• rs766444513
• NM_001145268.2:c.175C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-102749382-C-A
• chr7-102749382-C-T

Variant summary

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

The NM_001145268.2(FAM185A):​c.175C>A​(p.Pro59Thr) 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. 13/20 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. P59L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM185A NM_001145268.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

FAM185A (HGNC:22412): (family with sequence similarity 185 member A)

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=0.08300564).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM185A	NM_001145268.2	c.175C>A	p.Pro59Thr	missense_variant	Exon 1 of 8	ENST00000413034.3	NP_001138740.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM185A	ENST00000413034.3	c.175C>A	p.Pro59Thr	missense_variant	Exon 1 of 8	5	NM_001145268.2	ENSP00000395340.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.052	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0018	.;.;T
Eigen	Benign	-0.96
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.73	T;T;T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.083	T;T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	2.0	M;.;M
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	0.87	N;N;N
REVEL	Benign	0.14
Sift	Benign	0.29	T;T;T
Sift4G	Uncertain	0.059	T;T;T
Polyphen		0.39	B;.;B
Vest4		0.086
MutPred		0.22		Gain of phosphorylation at P59 (P = 0.0021);Gain of phosphorylation at P59 (P = 0.0021);Gain of phosphorylation at P59 (P = 0.0021);
MVP		0.072
ClinPred		0.11	T
GERP RS		0.94
Varity_R		0.034
gMVP		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs766444513; hg19: chr7-102389829;