rs1329933435

Variant names:

• chr7-102749383-C-A
• rs1329933435
• NM_001145268.2:c.176C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-102749383-C-A
• chr7-102749383-C-T

Variant summary

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

The NM_001145268.2(FAM185A):​c.176C>A​(p.Pro59Gln) 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. 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. P59S) 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: -1.28
• Publications: 0 publications found

Genes affected

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

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=0.12140453).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM185A	NM_001145268.2	c.176C>A	p.Pro59Gln	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.176C>A	p.Pro59Gln	missense_variant	Exon 1 of 8	5	NM_001145268.2	ENSP00000395340.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00 AC: 0 AN: 149192 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

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	0.084
BayesDel_addAF	Benign	-0.060	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	0.78
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0048	.;.;T
Eigen	Benign	-0.81
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.060	N
LIST_S2	Benign	0.69	T;T;T
M_CAP	Uncertain	0.15	D
MetaRNN	Benign	0.12	T;T;T
MetaSVM	Benign	-0.71	T
MutationAssessor	Benign	1.6	L;.;L
PhyloP100		-1.3
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	0.39	N;N;N
REVEL	Benign	0.15
Sift	Uncertain	0.011	D;D;T
Sift4G	Benign	0.074	T;T;T
Polyphen		0.041	B;.;P
Vest4		0.13
MutPred		0.18		Loss of glycosylation at P59 (P = 0.0049);Loss of glycosylation at P59 (P = 0.0049);Loss of glycosylation at P59 (P = 0.0049);
MVP		0.081
ClinPred		0.32	T
GERP RS		-0.53
PromoterAI		-0.042	Neutral
Varity_R		0.029
gMVP		0.27
Mutation Taster		=98/2	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: rs1329933435; hg19: chr7-102389830;