rs17627049

Variant names:

• chr6-33570025-C-A
• rs17627049
• ENST00000612409.1:n.200-738C>A

Variant summary

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

The ENST00000612409.1(GGNBP1):​n.200-738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,914 control chromosomes in the GnomAD database, including 3,714 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 0.21 (3714 hom., cov: 30)
• Consequence: GGNBP1 ENST00000612409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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.200-738C>A		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31731 AN: 151796 Hom.: 3713 Cov.: 30

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.209 AC: 31750 AN: 151914 Hom.: 3714 Cov.: 30 AF XY: 0.200 AC XY: 14858 AN XY: 74260

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.219

Alfa AF: 0.252 Hom.: 4815

Bravo AF: 0.213

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17627049; hg19: chr6-33537802;