7-66858513-T-C

Variant names:

• chr7-66858513-T-C
• rs2016325
• ENST00000727959.1:n.964+378T>C

Variant summary

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

The ENST00000727959.1(ENSG00000289177):​n.964+378T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,096 control chromosomes in the GnomAD database, including 15,801 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 0.42 (15801 hom., cov: 32)
• Consequence: ENSG00000289177 ENST00000727959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 8 publications found

Genes affected

ENSG00000289177 (HGNC:):

GTF2IP23 (HGNC:51735): (general transcription factor IIi pseudogene 23)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GTF2IP23	NR_135738.1	n.350+378T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289177	ENST00000727959.1	n.964+378T>C		intron_variant	Intron 6 of 9
ENSG00000289177	ENST00000727960.1	n.923+378T>C		intron_variant	Intron 5 of 15
ENSG00000289177	ENST00000727961.1	n.372+13131T>C		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64115 AN: 151978 Hom.: 15803 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.422 AC: 64110 AN: 152096 Hom.: 15801 Cov.: 32 AF XY: 0.420 AC XY: 31216 AN XY: 74340

African (AFR) AF: 0.178 AC: 7389 AN: 41490

American (AMR) AF: 0.470 AC: 7179 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.186 AC: 966 AN: 5184

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4824

European-Finnish (FIN) AF: 0.523 AC: 5526 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38277 AN: 67994

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.499 Hom.: 28053

Bravo AF: 0.404

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2016325; hg19: chr7-66323500;