NM_173537.5:c.1692C>A

Variant names:

• chr7-74797820-G-T
• NM_173537.5:c.1692C>A
• GTF2IRD2 p.Ala564Ala

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_173537.5(GTF2IRD2):​c.1692C>A​(p.Ala564Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A564A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 16)
• Consequence: GTF2IRD2 NM_173537.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 0 publications found

Genes affected

GTF2IRD2 (HGNC:30775): (GTF2I repeat domain containing 2) This gene is one of several closely related genes on chromosome 7 encoding proteins containing helix-loop-helix motifs. These proteins may function as regulators of transcription. The encoded protein is unique in that its C-terminus is derived from CHARLIE8 transposable element sequence. This gene is located in a region of chromosome 7 that is deleted in Williams-Beuren syndrome, and loss of this locus may contribute to the cognitive phenotypes observed in this disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ENSG00000289346 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP7: Synonymous conserved (PhyloP=0.302 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173537.5. 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
	GTF2IRD2	NM_173537.5	MANE Select	c.1692C>A	p.Ala564Ala	synonymous	Exon 16 of 16	NP_775808.4
	GTF2IRD2	NM_001368300.2		c.2178C>A	p.Ala726Ala	synonymous	Exon 17 of 17	NP_001355229.1	A0A494C0I1
	GTF2IRD2	NM_001388079.1		c.1707C>A	p.Ala569Ala	synonymous	Exon 16 of 16	NP_001375008.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF2IRD2	ENST00000451013.7	TSL:1 MANE Select	c.1692C>A	p.Ala564Ala	synonymous	Exon 16 of 16	ENSP00000406723.3	Q86UP8-1
	ENSG00000289346	ENST00000625377.3	TSL:5	c.1692C>A	p.Ala564Ala	synonymous	Exon 23 of 23	ENSP00000486581.2
	GTF2IRD2	ENST00000651129.1		c.2178C>A	p.Ala726Ala	synonymous	Exon 17 of 17	ENSP00000498563.1	A0A494C0I1

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 19

GnomAD4 genome Cov.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		0.30

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

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

Other links and lift over

hg19: chr7-74212159;