rs722525

Variant names:

• chr10-118340102-G-T
• rs722525
• NM_022063.3:c.-9+1625C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022063.3(FAM204A):​c.-9+1625C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,056 control chromosomes in the GnomAD database, including 3,591 homozygotes. 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: 𝑓 0.21 (3591 hom., cov: 32)
• Consequence: FAM204A NM_022063.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 5 publications found

Genes affected

FAM204A (HGNC:25794): (family with sequence similarity 204 member A)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022063.3. 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
	FAM204A	NM_022063.3	MANE Select	c.-9+1625C>A		intron	N/A	NP_071346.1	Q9H8W3
	FAM204A	NM_001134672.2		c.-9+2168C>A		intron	N/A	NP_001128144.1	Q9H8W3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM204A	ENST00000369183.9	TSL:1 MANE Select	c.-9+1625C>A		intron	N/A	ENSP00000358183.4	Q9H8W3
	FAM204A	ENST00000369172.8	TSL:3	c.-9+2168C>A		intron	N/A	ENSP00000358170.4	Q9H8W3
	FAM204A	ENST00000885074.1		c.-188+1625C>A		intron	N/A	ENSP00000555133.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31453 AN: 151938 Hom.: 3596 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31431 AN: 152056 Hom.: 3591 Cov.: 32 AF XY: 0.215 AC XY: 15977 AN XY: 74330

African (AFR) AF: 0.154 AC: 6389 AN: 41504

American (AMR) AF: 0.141 AC: 2153 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4820

European-Finnish (FIN) AF: 0.376 AC: 3962 AN: 10540

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14708 AN: 67966

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.211 Hom.: 1963

Bravo AF: 0.185

Asia WGS AF: 0.235 AC: 816 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.39
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

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: rs722525; hg19: chr10-120099614;