6-33580617-G-T

Variant names:

• chr6-33580617-G-T
• rs5745568
• ENST00000612409.1:n.363-3249G>T

Variant summary

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

The ENST00000612409.1(GGNBP1):​n.363-3249G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,212 control chromosomes in the GnomAD database, including 3,278 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 0.19 (3278 hom., cov: 33)
• Consequence: GGNBP1 ENST00000612409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

GGNBP1 (HGNC:19427): (gametogenetin binding protein 1 (pseudogene)) This gene is the ortholog of the mouse gametogenetin-binding protein 1 gene. In human, the open reading frame is disrupted by a nonsense mutation after 8-aa; consequently, this gene is currently considered to be a unitary pseudogene in human even though it is functional in other mammals. [provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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
GGNBP1	ENST00000612409.1	n.363-3249G>T		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29231 AN: 152094 Hom.: 3268 Cov.: 33

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.192 AC: 29273 AN: 152212 Hom.: 3278 Cov.: 33 AF XY: 0.203 AC XY: 15118 AN XY: 74408

Gnomad4 AFR AF: 0.0964

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.170

Alfa AF: 0.202 Hom.: 6606

Bravo AF: 0.182

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5745568; hg19: chr6-33548394;