rs1388565733

Variant names:

• chr6-17600683-G-A
• rs1388565733
• NM_016255.3:c.274G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-17600683-G-A
• chr6-17600683-G-C
• chr6-17600683-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016255.3(FAM8A1):​c.274G>A​(p.Gly92Ser) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G92R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM8A1 NM_016255.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 0 publications found

Genes affected

FAM8A1 (HGNC:16372): (family with sequence similarity 8 member A1) Predicted to be involved in ubiquitin-dependent ERAD pathway. Part of Hrd1p ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286885 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.043525606).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM8A1	NM_016255.3	c.274G>A	p.Gly92Ser	missense_variant	Exon 1 of 5	ENST00000259963.4	NP_057339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM8A1	ENST00000259963.4	c.274G>A	p.Gly92Ser	missense_variant	Exon 1 of 5	1	NM_016255.3	ENSP00000259963.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.92
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.052	N
LIST_S2	Benign	0.45	T
M_CAP	Benign	0.082	D
MetaRNN	Benign	0.044	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.76
PrimateAI	Pathogenic	0.81	D
PROVEAN	Benign	0.17	N
REVEL	Benign	0.014
Sift	Benign	0.49	T
Sift4G	Benign	0.34	T
Polyphen		0.0020	B
Vest4		0.038
MutPred		0.077		Gain of phosphorylation at G92 (P = 0.0177);
MVP		0.21
MPC		0.31
ClinPred		0.053	T
GERP RS		1.4
PromoterAI		-0.012	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.037
gMVP		0.23
Mutation Taster		=96/4	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: rs1388565733; hg19: chr6-17600914;