rs2023229

Variant names:

• chr16-29361043-G-T
• rs2023229
• ENST00000502626.1:n.249-207G>T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ENSG00000290680 (HGNC:):

SNX29P2 (HGNC:31914): (sorting nexin 29 pseudogene 2)

ACMG classification

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
SNX29P2	NR_002939.3	n.964-207G>T		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290680	ENST00000502626.1	n.249-207G>T		intron_variant	Intron 1 of 2	2
ENSG00000290680	ENST00000507381.5	n.498-207G>T		intron_variant	Intron 3 of 5	5
ENSG00000290680	ENST00000509141.5	n.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

Other links and lift over

dbSNP: rs2023229; hg19: chr16-29372364;