TCAF2 p.Pro730Pro

Variant names:

• chr7-143724379-C-C
• NM_001363538.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr7-143724380--
• chr7-143724382-C-T
• chr7-143724382-C-A
• chr7-143724382-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001363538.2(TCAF2):​c. variant causes a intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 20)
• Consequence: TCAF2 NM_001363538.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.40
• Publications: 0 publications found

Genes affected

TCAF2 (HGNC:26878): (TRPM8 channel associated factor 2) Enables transmembrane transporter binding activity. Involved in negative regulation of anion channel activity; positive regulation of cell migration; and positive regulation of protein targeting to membrane. Located in cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000291149 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363538.2. 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
	TCAF2	NM_001363538.2	MANE Select	c.		intron	N/A	NP_001350467.1	A6NFQ2-1
	TCAF2	NM_001438662.2		c.		intron	N/A	NP_001425591.2
	TCAF2	NM_001438663.2		c.		intron	N/A	NP_001425592.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCAF2	ENST00000684770.1	MANE Select	c.		intron	N/A	ENSP00000506869.1	A6NFQ2-1
	TCAF2	ENST00000441159.7	TSL:5	c.		intron	N/A	ENSP00000404265.2	A6NFQ2-1
	TCAF2	ENST00000411935.5	TSL:5	c.		intron	N/A	ENSP00000389100.1	A6NFQ2-3

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.4

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: chr7-143421472;