rs117026326

Positions:

• chr7-74711703-C-T

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GTF2I	NM_032999.4	c.763+594C>T		intron_variant		ENST00000573035.6	NP_127492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GTF2I	ENST00000573035.6	c.763+594C>T		intron_variant		1	NM_032999.4	ENSP00000460070.1

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

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.00622

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.0942

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0438

Gnomad4 NFE AF: 0.0129

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0165 Hom.: 5

Bravo AF: 0.0122

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.74
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

Publications

LitVar

Other links and lift over

dbSNP: rs117026326; hg19: chr7-74126034;