rs117026326

Variant names:

• chr7-74711703-C-T
• rs117026326
• NM_032999.4:c.763+594C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032999.4(GTF2I):​c.763+594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 152,172 control chromosomes in the GnomAD database, including 52 homozygotes. 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: 𝑓 0.014 (52 hom., cov: 32)
• Consequence: GTF2I NM_032999.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 40 publications found

Genes affected

GTF2I (HGNC:4659): (general transcription factor IIi) This gene encodes a phosphoprotein containing six characteristic repeat motifs. The encoded protein binds to the initiator element (Inr) and E-box element in promoters and functions as a regulator of transcription. This locus, along with several other neighboring genes, is deleted in Williams-Beuren syndrome. There are many closely related genes and pseudogenes for this gene on chromosome 7. This gene also has pseudogenes on chromosomes 9, 13, and 21. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2013]

GTF2I-AS1 (HGNC:55572): (GTF2I antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032999.4. 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
	GTF2I	NM_032999.4	MANE Select	c.763+594C>T		intron	N/A	NP_127492.1	P78347-1
	GTF2I	NM_033000.4		c.763+594C>T		intron	N/A	NP_127493.1	P78347-3
	GTF2I	NM_033001.4		c.763+594C>T		intron	N/A	NP_127494.1	P78347-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF2I	ENST00000573035.6	TSL:1 MANE Select	c.763+594C>T		intron	N/A	ENSP00000460070.1	P78347-1
	GTF2I	ENST00000614986.4	TSL:1	c.763+594C>T		intron	N/A	ENSP00000484526.1	P78347-3
	GTF2I	ENST00000621734.4	TSL:1	c.763+594C>T		intron	N/A	ENSP00000482476.1	P78347-4

Frequencies

GnomAD3 genomes AF: 0.0139 AC: 2111 AN: 152054 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00167

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.00623

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0139 AC: 2112 AN: 152172 Hom.: 52 Cov.: 32 AF XY: 0.0155 AC XY: 1150 AN XY: 74384

African (AFR) AF: 0.00166 AC: 69 AN: 41532

American (AMR) AF: 0.00622 AC: 95 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.0942 AC: 488 AN: 5178

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4822

European-Finnish (FIN) AF: 0.0438 AC: 463 AN: 10574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0129 AC: 874 AN: 68006

Other (OTH) AF: 0.0109 AC: 23 AN: 2106

Alfa AF: 0.0141 Hom.: 52

Bravo AF: 0.0122

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.094
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs117026326; hg19: chr7-74126034;