rs2215100

chrX-26676923-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000674719.1(VENTXP1):n.622+114324C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.60 (14104 hom., 19160 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: VENTXP1 ENST00000674719.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

Genes affected

VENTXP1 (HGNC:30900): (VENT homeobox pseudogene 1) 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd at 14109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VENTXP1	ENST00000674719.1	n.622+114324C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.600 AC: 65521 AN: 109203 Hom.: 14109 Cov.: 22 AF XY: 0.606 AC XY: 19130 AN XY: 31581

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.599

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.600 AC: 65548 AN: 109251 Hom.: 14104 Cov.: 22 AF XY: 0.606 AC XY: 19160 AN XY: 31639

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.603

Alfa AF: 0.577 Hom.: 5789

Bravo AF: 0.613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215100; hg19: chrX-26695040;