rs800606

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-21406342-C-G
• chr3-21406342-C-A
• chr3-21406342-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000475503.1(VENTXP7):​n.606C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: VENTXP7 ENST00000475503.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VENTXP7	NR_002311.1	n.617C>G		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>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 498148 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 272144

African (AFR) AF: 0.00 AC: 0 AN: 14238

American (AMR) AF: 0.00 AC: 0 AN: 32390

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16168

East Asian (EAS) AF: 0.00 AC: 0 AN: 24718

South Asian (SAS) AF: 0.00 AC: 0 AN: 63636

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29892

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2120

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 289360

Other (OTH) AF: 0.00 AC: 0 AN: 25626

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs440905; hg19: chr3-21447834;