NM_021806.4:c.163A>C

Variant names:

• chrX-154508586-T-G
• rs929283877
• NM_021806.4:c.163A>C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_021806.4(FAM3A):​c.163A>C​(p.Arg55Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000928 in 1,077,093 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 9.3e-7 (0 hom. 0 hem.)
• Consequence: FAM3A NM_021806.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 0 publications found

Genes affected

FAM3A (HGNC:13749): (FAM3 metabolism regulating signaling molecule A) This gene encodes a cytokine-like protein. The expression of this gene may be regulated by peroxisome proliferator-activated receptor gamma, and the encoded protein may be involved in the regulation of glucose and lipid metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP7: Synonymous conserved (PhyloP=1.96 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021806.4. 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
	FAM3A	NM_021806.4	MANE Select	c.163A>C	p.Arg55Arg	synonymous	Exon 4 of 9	NP_068578.2	P98173-1
	FAM3A	NM_001282311.2		c.205A>C	p.Arg69Arg	synonymous	Exon 5 of 10	NP_001269240.1	D3DWX8
	FAM3A	NM_001363822.2		c.163A>C	p.Arg55Arg	synonymous	Exon 5 of 10	NP_001350751.1	Q5HY75

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM3A	ENST00000447601.7	TSL:1 MANE Select	c.163A>C	p.Arg55Arg	synonymous	Exon 4 of 9	ENSP00000416146.2	P98173-1
	FAM3A	ENST00000858761.1		c.163A>C	p.Arg55Arg	synonymous	Exon 4 of 9	ENSP00000528820.1
	FAM3A	ENST00000858759.1		c.211A>C	p.Arg71Arg	synonymous	Exon 4 of 9	ENSP00000528818.1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 9.28e-7 AC: 1 AN: 1077093 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 349807

African (AFR) AF: 0.00 AC: 0 AN: 26099

American (AMR) AF: 0.00 AC: 0 AN: 31924

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18888

East Asian (EAS) AF: 0.00 AC: 0 AN: 29374

South Asian (SAS) AF: 0.00 AC: 0 AN: 51363

European-Finnish (FIN) AF: 0.0000259 AC: 1 AN: 38676

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4108

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 831337

Other (OTH) AF: 0.00 AC: 0 AN: 45324

GnomAD4 genome Cov.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	9.2
DANN	Benign	0.61
PhyloP100		2.0

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: rs929283877; hg19: chrX-153736917;