7-23521766-AC-GT

Variant names:

• chr7-23521766-AC-GT
• NM_013293.5:c.110_111delGTinsAC
• TRA2A p.Arg37His

Variant summary

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

The NM_013293.5(TRA2A):​c.110_111delGTinsAC​(p.Arg37His) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R37L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TRA2A NM_013293.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09
• Publications: 0 publications found

Genes affected

TRA2A (HGNC:16645): (transformer 2 alpha homolog) This gene is a member of the transformer 2 homolog family and encodes a protein with several RRM (RNA recognition motif) domains. This phosphorylated nuclear protein binds to specific RNA sequences and plays a role in the regulation of pre-mRNA splicing. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013293.5. 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
	TRA2A	NM_013293.5	MANE Select	c.110_111delGTinsAC	p.Arg37His	missense	N/A	NP_037425.1	Q13595-1
	TRA2A	NM_001362759.2		c.110_111delGTinsAC	p.Arg37His	missense	N/A	NP_001349688.1
	TRA2A	NM_001282757.2		c.-194_-193delGTinsAC		5_prime_UTR	Exon 3 of 9	NP_001269686.1	Q13595-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRA2A	ENST00000297071.9	TSL:1 MANE Select	c.110_111delGTinsAC	p.Arg37His	missense	N/A	ENSP00000297071.4	Q13595-1
	TRA2A	ENST00000490942.1	TSL:1	n.578_579delGTinsAC		non_coding_transcript_exon	Exon 3 of 5
	TRA2A	ENST00000494255.5	TSL:1	n.859_860delGTinsAC		non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.1

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: chr7-23561385;