10-5641912-CGC-AGT

Variant names:

• chr10-5641912-CGC-AGT
• NM_024701.4:c.565_567delGCGinsACT
• ASB13 p.Ala189Thr

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_024701.4(ASB13):​c.565_567delGCGinsACT​(p.Ala189Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ASB13 NM_024701.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.34
• Publications: 0 publications found

Genes affected

ASB13 (HGNC:19765): (ankyrin repeat and SOCS box containing 13) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. They contain ankyrin repeat sequence and a SOCS box domain. The SOCS box serves to couple suppressor of cytokine signalling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants, both protein-coding and not protein-coding, have been described for this gene. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024701.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB13	NM_024701.4	MANE Select	c.565_567delGCGinsACT	p.Ala189Thr	missense	N/A	NP_078977.2
	ASB13	NR_024581.2		n.458_460delGCGinsACT		non_coding_transcript_exon	Exon 4 of 5
	ASB13	NR_037164.2		n.690_692delGCGinsACT		non_coding_transcript_exon	Exon 6 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB13	ENST00000357700.11	TSL:1 MANE Select	c.565_567delGCGinsACT	p.Ala189Thr	missense	N/A	ENSP00000350331.6	Q8WXK3-1
	ASB13	ENST00000459912.5	TSL:1	n.*124_*126delGCGinsACT		non_coding_transcript_exon	Exon 6 of 7	ENSP00000433358.1	Q8WXK3-2
	ASB13	ENST00000459912.5	TSL:1	n.*124_*126delGCGinsACT		3_prime_UTR	Exon 6 of 7	ENSP00000433358.1	Q8WXK3-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-5683875;