11-6718905-G-A

Position:

• chr11-6718905-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_003945.1(GVINP1):​n.2975C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.168 in 456,642 control chromosomes in the GnomAD database, including 8,353 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 0.15 (2173 hom., cov: 33)
  • Exomes 𝑓: 0.17 (6180 hom.)
• Consequence: GVINP1 NR_003945.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.37

Genes affected

(HGNC:):

GVINP1 (HGNC:25813): (GTPase, very large interferon inducible pseudogene 1) Predicted to enable GTP binding activity. Predicted to be located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GVINP1	NR_003945.1	n.2975C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000526769.3	n.3069C>T		non_coding_transcript_exon_variant	2/2	1
GVINP1	ENST00000531871.3	n.2976C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23206 AN: 152090 Hom.: 2163 Cov.: 33

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.144

GnomAD3 exomes AF: 0.199 AC: 27740 AN: 139250 Hom.: 3882 AF XY: 0.184 AC XY: 13857 AN XY: 75368

Gnomad AFR exome AF: 0.0835

Gnomad AMR exome AF: 0.434

Gnomad ASJ exome AF: 0.136

Gnomad EAS exome AF: 0.218

Gnomad SAS exome AF: 0.119

Gnomad FIN exome AF: 0.151

Gnomad NFE exome AF: 0.156

Gnomad OTH exome AF: 0.167

GnomAD4 exome AF: 0.175 AC: 53270 AN: 304432 Hom.: 6180 Cov.: 0 AF XY: 0.164 AC XY: 28503 AN XY: 173346

Gnomad4 AFR exome AF: 0.0869

Gnomad4 AMR exome AF: 0.432

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.150

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.153

GnomAD4 genome AF: 0.153 AC: 23226 AN: 152210 Hom.: 2173 Cov.: 33 AF XY: 0.154 AC XY: 11486 AN XY: 74424

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.147

Alfa AF: 0.171 Hom.: 1344

Bravo AF: 0.162

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10839601; hg19: chr11-6740136;