11-126235083-CCC-TCA

Variant names:

• chr11-126235083-CCC-TCA
• NM_024556.4:c.82_84delCCCinsTCA
• FAM118B p.Pro28Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024556.4(FAM118B):​c.82_84delCCCinsTCA​(p.Pro28Ser) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM118B NM_024556.4 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.19
• Publications: 0 publications found

Genes affected

FAM118B (HGNC:26110): (family with sequence similarity 118 member B) Enables identical protein binding activity. Predicted to be involved in Cajal body organization. Predicted to be located in Cajal body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024556.4. 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
	FAM118B	NM_024556.4	MANE Select	c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	NP_078832.1	Q9BPY3
	FAM118B	NM_001439324.1		c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	NP_001426253.1
	FAM118B	NM_001330446.2		c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	NP_001317375.1	J3KP39

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM118B	ENST00000533050.6	TSL:1 MANE Select	c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	ENSP00000433343.1	Q9BPY3
	FAM118B	ENST00000891485.1		c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	ENSP00000561544.1
	FAM118B	ENST00000891481.1		c.82_84delCCCinsTCA	p.Pro28Ser	missense splice_region	N/A	ENSP00000561540.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr11-126104978;