10-29445302-C-T

Variant names:

• chr10-29445302-C-T
• rs10610693
• ENST00000413405.6:n.181+29890C>T

Variant summary

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

The ENST00000413405.6(SVIL-AS1):​n.181+29890C>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: 13)
• Consequence: SVIL-AS1 ENST00000413405.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

SVIL-AS1 (HGNC:):

SVIL-AS1 (HGNC:51219): (SVIL antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SVIL-AS1	NR_110920.1	n.207-12972C>T		intron_variant	Intron 2 of 3
SVIL-AS1	NR_110921.1	n.206+29890C>T		intron_variant	Intron 2 of 2
SVIL-AS1	NR_110922.1	n.181+29890C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVIL-AS1	ENST00000413405.6	n.181+29890C>T		intron_variant	Intron 2 of 2	1
SVIL-AS1	ENST00000414457.6	n.206+29890C>T		intron_variant	Intron 2 of 2	1
SVIL-AS1	ENST00000423223.6	n.181+29890C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 13

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 13

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.44
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10610693; hg19: chr10-29734231;