rs409974

chr3-21405844-G-A

Variant summary

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

The NR_002311.1(VENTXP7):n.119G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 825,252 control chromosomes in the GnomAD database, including 4,533 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 0.12 (1216 hom., cov: 32)
  • Exomes 𝑓: 0.090 (3317 hom.)
• Consequence: VENTXP7 NR_002311.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

VENTXP7 (HGNC:13638): (VENT homeobox pseudogene 7) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This pseudogene is a member of the Vent homeobox gene family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VENTXP7	NR_002311.1	n.119G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VENTXP7	ENST00000475503.1	n.108G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18687 AN: 151888 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000588

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.0898 AC: 60455 AN: 673246 Hom.: 3317 Cov.: 9 AF XY: 0.0879 AC XY: 31001 AN XY: 352668

Gnomad4 AFR exome AF: 0.0898

Gnomad4 AMR exome AF: 0.0533

Gnomad4 ASJ exome AF: 0.0868

Gnomad4 EAS exome AF: 0.000345

Gnomad4 SAS exome AF: 0.0364

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.0910

GnomAD4 genome AF: 0.123 AC: 18687 AN: 152006 Hom.: 1216 Cov.: 32 AF XY: 0.116 AC XY: 8635 AN XY: 74288

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0945

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000590

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.106

Alfa AF: 0.137 Hom.: 185

Bravo AF: 0.121

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs409974; hg19: chr3-21447336;