rs73366469

Variant names:

• chr7-74619286-T-C
• rs73366469
• ENST00000789967.1:n.496-2020A>G

Variant summary

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

The ENST00000789967.1(GTF2I-AS1):​n.496-2020A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,182 control chromosomes in the GnomAD database, including 1,191 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 0.12 (1191 hom., cov: 31)
• Consequence: GTF2I-AS1 ENST00000789967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 26 publications found

Genes affected

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 (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789967.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF2I-AS1	ENST00000789967.1		n.496-2020A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17633 AN: 152064 Hom.: 1183 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0661

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.116 AC: 17677 AN: 152182 Hom.: 1191 Cov.: 31 AF XY: 0.114 AC XY: 8473 AN XY: 74386

African (AFR) AF: 0.169 AC: 7031 AN: 41528

American (AMR) AF: 0.0805 AC: 1230 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.118 AC: 611 AN: 5172

South Asian (SAS) AF: 0.122 AC: 588 AN: 4818

European-Finnish (FIN) AF: 0.0653 AC: 692 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6698 AN: 68004

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.105 Hom.: 413

Bravo AF: 0.119

Asia WGS AF: 0.111 AC: 388 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	0.49
DANN	Benign	0.72
PhyloP100		-2.6

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

dbSNP: rs73366469;

hg19: chr7-74033600;