rs2023229

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000502626.1(ENSG00000290680):​n.249-207G>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: not found (cov: 18)

Consequence

ENSG00000290680
ENST00000502626.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23
Variant links:
Genes affected
SNX29P2 (HGNC:31914): (sorting nexin 29 pseudogene 2)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX29P2NR_002939.3 linkn.964-207G>T intron_variant Intron 7 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000290680ENST00000502626.1 linkn.249-207G>T intron_variant Intron 1 of 2 2
ENSG00000290680ENST00000507381.5 linkn.498-207G>T intron_variant Intron 3 of 5 5
ENSG00000290680ENST00000509141.5 linkn.330-207G>T intron_variant Intron 3 of 3 5

Frequencies

GnomAD3 genomes
Cov.:
18
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.74
DANN
Benign
0.25

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2023229; hg19: chr16-29372364; API