3-21406342-C-T

Variant names:

• chr3-21406342-C-T
• rs440905
• ENST00000475503.1:n.606C>T

Variant summary

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

The NR_002311.1(VENTXP7):​n.617C>T 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 0.627 in 649,204 control chromosomes in the GnomAD database, including 131,824 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 0.66 (34477 hom., cov: 31)
  • Exomes 𝑓: 0.62 (97347 hom.)
• Consequence: VENTXP7 NR_002311.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VENTXP7	NR_002311.1	n.617C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VENTXP7	ENST00000475503.1	n.606C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100159 AN: 151782 Hom.: 34422 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.635

GnomAD4 exome AF: 0.617 AC: 306745 AN: 497306 Hom.: 97347 Cov.: 6 AF XY: 0.619 AC XY: 168100 AN XY: 271690

Gnomad4 AFR exome AF: 0.850

Gnomad4 AMR exome AF: 0.697

Gnomad4 ASJ exome AF: 0.655

Gnomad4 EAS exome AF: 0.895

Gnomad4 SAS exome AF: 0.691

Gnomad4 FIN exome AF: 0.534

Gnomad4 NFE exome AF: 0.562

Gnomad4 OTH exome AF: 0.619

GnomAD4 genome AF: 0.660 AC: 100270 AN: 151898 Hom.: 34477 Cov.: 31 AF XY: 0.660 AC XY: 49007 AN XY: 74206

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.635

Alfa AF: 0.550 Hom.: 4257

Bravo AF: 0.681

Asia WGS AF: 0.805 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs440905; hg19: chr3-21447834;