rs55932017

Variant names:

• chr5-148982157-ATT-A
• rs55932017
• NM_024577.4:c.*22552_*22553delAA

Your query was ambiguous. Multiple possible variants found:

• chr5-148982157-ATT-A
• chr5-148982157-ATT-AT
• chr5-148982157-ATT-ATTT
• chr5-148982157-ATT-ATTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_024577.4(SH3TC2):​c.*22552_*22553delAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: SH3TC2 NM_024577.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

SH3TC2 (HGNC:29427): (SH3 domain and tetratricopeptide repeats 2) This gene encodes a protein with two N-terminal Src homology 3 (SH3) domains and 10 tetratricopeptide repeat (TPR) motifs, and is a member of a small gene family. The gene product has been proposed to be an adapter or docking molecule. Mutations in this gene result in autosomal recessive Charcot-Marie-Tooth disease type 4C, a childhood-onset neurodegenerative disease characterized by demyelination of motor and sensory neurons. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3TC2	NM_024577.4	c.*22552_*22553delAA		3_prime_UTR_variant	Exon 17 of 17	ENST00000515425.6	NP_078853.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3TC2	ENST00000515425	c.*22552_*22553delAA		3_prime_UTR_variant	Exon 17 of 17	1	NM_024577.4	ENSP00000423660.1
SH3TC2	ENST00000504690.5	n.*12+21567_*12+21568delAA		intron_variant	Intron 17 of 19	5		ENSP00000425627.1
SH3TC2	ENST00000510350.1	n.231+24722_231+24723delAA		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55932017; hg19: chr5-148361720;