chrX-8795299-C-A

Variant names:

• chrX-8795299-C-A
• NM_174951.3:c.610G>T

Variant summary

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

The NM_174951.3(FAM9A):​c.610G>T​(p.Ala204Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000918 in 1,088,863 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. 13/18 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. A204T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 9.2e-7 (0 hom. 0 hem.)
• Consequence: FAM9A NM_174951.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

FAM9A (HGNC:18403): (family with sequence similarity 9 member A) This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be a nuclear protein that is localized to the nucleolus, and has some similarity to a synaptonemal complex protein. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Aug 2011]

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=0.08073309).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM9A	NM_174951.3	c.610G>T	p.Ala204Ser	missense_variant	Exon 7 of 10	ENST00000381003.7	NP_777611.1
FAM9A	NM_001171186.1	c.610G>T	p.Ala204Ser	missense_variant	Exon 7 of 10		NP_001164657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM9A	ENST00000381003.7	c.610G>T	p.Ala204Ser	missense_variant	Exon 7 of 10	1	NM_174951.3	ENSP00000370391.3
FAM9A	ENST00000543214.1	c.610G>T	p.Ala204Ser	missense_variant	Exon 7 of 10	1		ENSP00000440163.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 9.18e-7 AC: 1 AN: 1088863 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 357075

Gnomad4 AFR exome AF: 0.0000381

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.4
DANN	Benign	0.95
DEOGEN2	Benign	0.0070	T;T
FATHMM_MKL	Benign	0.0047	N
LIST_S2	Benign	0.24	T;.
M_CAP	Benign	0.00061	T
MetaRNN	Benign	0.081	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.0	L;L
PROVEAN	Benign	-0.11	N;N
REVEL	Benign	0.020
Sift	Benign	0.35	T;T
Sift4G	Uncertain	0.017	D;D
Polyphen		0.56	P;P
Vest4		0.16
MutPred		0.36		Gain of glycosylation at A204 (P = 5e-04);Gain of glycosylation at A204 (P = 5e-04);
MVP		0.46
MPC		0.050
ClinPred		0.11	T
GERP RS		0.15
Varity_R		0.13
gMVP		0.017

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-8763340;