chr6-118960167-G-C

Position:

• chr6-118960167-G-C

Variant summary

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

The NM_024581.6(FAM184A):​c.3359C>G​(p.Ala1120Gly) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM184A NM_024581.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.70

Genes affected

FAM184A (HGNC:20991): (family with sequence similarity 184 member A) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000253194 (HGNC:):

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=0.16092113).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM184A	NM_024581.6	c.3359C>G	p.Ala1120Gly	missense_variant	18/18	ENST00000338891.12	NP_078857.5
FAM184A	NM_001100411.3	c.2852C>G	p.Ala951Gly	missense_variant	17/17		NP_001093881.1
FAM184A	NM_001288576.2	c.2747C>G	p.Ala916Gly	missense_variant	16/16		NP_001275505.1
LOC124901389	XR_007059729.1	n.76+25177G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM184A	ENST00000338891.12	c.3359C>G	p.Ala1120Gly	missense_variant	18/18	1	NM_024581.6	ENSP00000342604.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 20, 2024

The c.3359C>G (p.A1120G) alteration is located in exon 18 (coding exon 18) of the FAM184A gene. This alteration results from a C to G substitution at nucleotide position 3359, causing the alanine (A) at amino acid position 1120 to be replaced by a glycine (G). 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
BayesDel_addAF	Benign	-0.099	T
BayesDel_noAF	Benign	-0.38
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.022	T;T;T;.;T;.;.
Eigen	Benign	0.16
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.78	T;T;T;T;T;T;T
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.16	T;T;T;T;T;T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.2	.;.;L;.;.;.;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.3	N;.;N;N;N;N;N
REVEL	Benign	0.12
Sift	Uncertain	0.023	D;.;T;T;T;T;T
Sift4G	Uncertain	0.034	D;T;T;T;T;T;T
Polyphen		0.94, 0.93	.;.;P;.;.;.;P
Vest4		0.17, 0.18, 0.25, 0.23, 0.26
MutPred		0.036		.;.;Loss of glycosylation at S1125 (P = 0.1671);.;.;.;.;
MVP		0.64
MPC		0.48
ClinPred		0.89	D
GERP RS		4.5
Varity_R		0.11
gMVP		0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: chr6-119281332;