rs4717322

Variant names:

• chr7-66813220-C-T
• rs4717322
• ENST00000457166.5:n.876-1677G>A

Variant summary

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

The ENST00000457166.5(GTF2IRD1P1):​n.876-1677G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,158 control chromosomes in the GnomAD database, including 1,581 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 0.13 (1581 hom., cov: 30)
• Consequence: GTF2IRD1P1 ENST00000457166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 7 publications found

Genes affected

GTF2IRD1P1 (HGNC:):

GTF2IRD1P1 (HGNC:44136): (GTF2I repeat domain containing 1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457166.5. 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
	GTF2IRD1P1	NR_003934.2		n.936-1677G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF2IRD1P1	ENST00000457166.5	TSL:2	n.876-1677G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20327 AN: 152040 Hom.: 1577 Cov.: 30

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.134 AC: 20340 AN: 152158 Hom.: 1581 Cov.: 30 AF XY: 0.132 AC XY: 9793 AN XY: 74398

African (AFR) AF: 0.0731 AC: 3034 AN: 41524

American (AMR) AF: 0.127 AC: 1944 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3464

East Asian (EAS) AF: 0.307 AC: 1583 AN: 5162

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10602

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10466 AN: 67990

Other (OTH) AF: 0.151 AC: 318 AN: 2112

Alfa AF: 0.151 Hom.: 8187

Bravo AF: 0.132

Asia WGS AF: 0.260 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		0.18

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: rs4717322;

hg19: chr7-66278207;