chr10-118310915-G-C

Variant names:

• chr10-118310915-G-C
• rs4751651
• NM_022063.3:c.651-7C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022063.3(FAM204A):​c.651-7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: FAM204A NM_022063.3 splice_region, intron
• Scores: Splicing: ADA: 0.00005235
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM204A	NM_022063.3	c.651-7C>G		splice_region_variant, intron_variant	Intron 8 of 8	ENST00000369183.9	NP_071346.1
FAM204A	NM_001134672.2	c.651-7C>G		splice_region_variant, intron_variant	Intron 7 of 7		NP_001128144.1
FAM204A	XM_005270024.2	c.672-7C>G		splice_region_variant, intron_variant	Intron 9 of 9		XP_005270081.1
FAM204A	XM_047425619.1	c.651-7C>G		splice_region_variant, intron_variant	Intron 9 of 9		XP_047281575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM204A	ENST00000369183.9	c.651-7C>G		splice_region_variant, intron_variant	Intron 8 of 8	1	NM_022063.3	ENSP00000358183.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000052
dbscSNV1_RF	Benign	0.028
SpliceAI score (max)		0.020		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: rs4751651; hg19: chr10-120070427;