5-149063517-T-G

Variant names:

• chr5-149063517-T-G
• rs7705960
• ENST00000507318.1:n.15T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000507318.1(SH3TC2-DT):​n.15T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SH3TC2-DT ENST00000507318.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 5 publications found

Genes affected

SH3TC2-DT (HGNC:52905): (SH3TC2 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3TC2-DT	NR_122044.1	n.201T>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3TC2-DT	ENST00000507318.1	n.15T>G		non_coding_transcript_exon_variant	Exon 1 of 2	2
SH3TC2-DT	ENST00000509139.1	n.63T>G		non_coding_transcript_exon_variant	Exon 1 of 3	2
SH3TC2-DT	ENST00000512007.2	n.231T>G		non_coding_transcript_exon_variant	Exon 1 of 4	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 7920 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4158

African (AFR) AF: 0.00 AC: 0 AN: 348

American (AMR) AF: 0.00 AC: 0 AN: 1430

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 110

East Asian (EAS) AF: 0.00 AC: 0 AN: 466

South Asian (SAS) AF: 0.00 AC: 0 AN: 686

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 112

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 12

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4394

Other (OTH) AF: 0.00 AC: 0 AN: 362

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.85
PhyloP100		-0.28
PromoterAI		-0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7705960; hg19: chr5-148443080;