rs4717322

chr7-66813220-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003934.2(GTF2IRD1P1):n.936-1677G>A variant causes a intron, non coding transcript 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 NR_003934.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GTF2IRD1P1	NR_003934.2	n.936-1677G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GTF2IRD1P1	ENST00000457166.5	n.876-1677G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0731

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.151

Alfa AF: 0.156 Hom.: 4094

Bravo AF: 0.132

Asia WGS AF: 0.260 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4717322; hg19: chr7-66278207;