21-13471119-A-G

Variant names:

• chr21-13471119-A-G
• rs459039
• ENST00000424290.1:n.100-13187T>C

Variant summary

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

The ENST00000424290.1(GTF2IP2):​n.100-13187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 148,476 control chromosomes in the GnomAD database, including 6,463 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 0.25 (6463 hom., cov: 29)
• Consequence: GTF2IP2 ENST00000424290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 0 publications found

Genes affected

GTF2IP2 (HGNC:16082): (general transcription factor IIi pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GTF2IP2	ENST00000424290.1	n.100-13187T>C		intron_variant	Intron 1 of 5	6

Frequencies

GnomAD3 genomes AF: 0.246 AC: 36450 AN: 148410 Hom.: 6466 Cov.: 29

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.246 AC: 36460 AN: 148476 Hom.: 6463 Cov.: 29 AF XY: 0.251 AC XY: 18080 AN XY: 72162

African (AFR) AF: 0.358 AC: 14260 AN: 39796

American (AMR) AF: 0.228 AC: 3368 AN: 14792

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 728 AN: 3458

East Asian (EAS) AF: 0.888 AC: 4356 AN: 4908

South Asian (SAS) AF: 0.367 AC: 1731 AN: 4716

European-Finnish (FIN) AF: 0.143 AC: 1408 AN: 9856

Middle Eastern (MID) AF: 0.281 AC: 81 AN: 288

European-Non Finnish (NFE) AF: 0.147 AC: 9934 AN: 67704

Other (OTH) AF: 0.267 AC: 547 AN: 2048

Alfa AF: 0.184 Hom.: 429

Bravo AF: 0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs459039; hg19: chr21-14843440;