rs722525

Positions:

• chr10-118340102-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM204A	NM_022063.3	c.-9+1625C>A		intron_variant		ENST00000369183.9	NP_071346.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM204A	ENST00000369183.9	c.-9+1625C>A		intron_variant		1	NM_022063.3	ENSP00000358183	P1

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.179

Alfa AF: 0.212 Hom.: 1813

Bravo AF: 0.185

Asia WGS AF: 0.235 AC: 816 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.39

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

LitVar

Other links and lift over

dbSNP: rs722525; hg19: chr10-120099614;