rs2215100

Variant names:

• chrX-26676923-C-T
• rs2215100
• ENST00000674719.1:n.622+114324C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000674719.1(VENTXP1):​n.622+114324C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 0 publications found

Genes affected

VENTXP1 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674719.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VENTXP1	ENST00000674719.1		n.622+114324C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 65521 AN: 109203 Hom.: 14109 Cov.: 22

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

African (AFR) AF: 0.559 AC: 16801 AN: 30068

American (AMR) AF: 0.719 AC: 7286 AN: 10127

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 1541 AN: 2613

East Asian (EAS) AF: 0.917 AC: 3166 AN: 3454

South Asian (SAS) AF: 0.803 AC: 2045 AN: 2547

European-Finnish (FIN) AF: 0.561 AC: 3161 AN: 5636

Middle Eastern (MID) AF: 0.578 AC: 119 AN: 206

European-Non Finnish (NFE) AF: 0.573 AC: 30041 AN: 52440

Other (OTH) AF: 0.603 AC: 902 AN: 1496

Alfa AF: 0.577 Hom.: 5789

Bravo AF: 0.613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2215100; hg19: chrX-26695040;