rs10839601

Variant names:

• chr11-6718905-G-A
• rs10839601
• ENST00000526769.4:n.3124C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000526769.4(ENSG00000291143):​n.3124C>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: ENSG00000291143 ENST00000526769.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.37
• Publications: 6 publications found

Genes affected

ENSG00000291143 (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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GVINP1	NR_003945.1	n.2975C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291143	ENST00000526769.4	n.3124C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
GVINP1	ENST00000531871.3	n.2976C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000294763	ENST00000725824.1	n.218-29272G>A		intron_variant	Intron 1 of 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

GnomAD2 exomes AF: 0.199 AC: 27740 AN: 139250 AF XY: 0.184

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 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

African (AFR) AF: 0.0869 AC: 749 AN: 8624

American (AMR) AF: 0.432 AC: 11783 AN: 27276

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 1495 AN: 10790

East Asian (EAS) AF: 0.215 AC: 1980 AN: 9208

South Asian (SAS) AF: 0.118 AC: 7047 AN: 59736

European-Finnish (FIN) AF: 0.150 AC: 1926 AN: 12808

Middle Eastern (MID) AF: 0.0734 AC: 204 AN: 2780

European-Non Finnish (NFE) AF: 0.163 AC: 25903 AN: 158948

Other (OTH) AF: 0.153 AC: 2183 AN: 14262

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

African (AFR) AF: 0.0850 AC: 3529 AN: 41532

American (AMR) AF: 0.290 AC: 4431 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1123 AN: 5180

South Asian (SAS) AF: 0.128 AC: 618 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11100 AN: 68012

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.166 Hom.: 1865

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
PhyloP100		6.4

Splicing

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

Other links and lift over

dbSNP: rs10839601; hg19: chr11-6740136;