5-148933204-T-C

Position:

• chr5-148933204-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504690.5(SH3TC2):​c.*226-9026A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,112 control chromosomes in the GnomAD database, including 8,986 homozygotes. 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: 𝑓 0.32 (8986 hom., cov: 32)
• Consequence: SH3TC2 ENST00000504690.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3TC2	ENST00000504690.5	c.*226-9026A>G		intron_variant, NMD_transcript_variant		5		ENSP00000425627

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49328 AN: 151994 Hom.: 8986 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.324 AC: 49349 AN: 152112 Hom.: 8986 Cov.: 32 AF XY: 0.326 AC XY: 24234 AN XY: 74378

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.0174

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.345

Alfa AF: 0.383 Hom.: 15997

Bravo AF: 0.302

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7729953; hg19: chr5-148312767;