NM_017772.4:c.337C>A

Variant names:

• chr6-37279527-C-A
• rs939167791
• NM_017772.4:c.337C>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_017772.4(TBC1D22B):​c.337C>A​(p.Arg113Arg) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TBC1D22B NM_017772.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 0 publications found

Genes affected

TBC1D22B (HGNC:21602): (TBC1 domain family member 22B) Enables 14-3-3 protein binding activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BP7: Synonymous conserved (PhyloP=0.463 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017772.4. 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
	TBC1D22B	NM_017772.4	MANE Select	c.337C>A	p.Arg113Arg	synonymous	Exon 3 of 13	NP_060242.2
	TBC1D22B	NR_130108.2		n.483C>A		non_coding_transcript_exon	Exon 3 of 13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D22B	ENST00000373491.3	TSL:1 MANE Select	c.337C>A	p.Arg113Arg	synonymous	Exon 3 of 13	ENSP00000362590.3	Q9NU19
	TBC1D22B	ENST00000942344.1		c.430C>A	p.Arg144Arg	synonymous	Exon 4 of 14	ENSP00000612403.1
	TBC1D22B	ENST00000869079.1		c.430C>A	p.Arg144Arg	synonymous	Exon 4 of 13	ENSP00000539138.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		0.46

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: rs939167791; hg19: chr6-37247303;