5-149063517-T-C

Position:

• chr5-149063517-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_122044.1(SH3TC2-DT):​n.201T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 159,894 control chromosomes in the GnomAD database, including 19,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.48 (18800 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1055 hom.)
• Consequence: SH3TC2-DT NR_122044.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.279

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 5-149063517-T-C is Benign according to our data. Variant chr5-149063517-T-C is described in ClinVar as [Benign]. Clinvar id is 684358.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3TC2-DT	NR_122044.1	n.201T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3TC2-DT	ENST00000507318.1	n.15T>C		non_coding_transcript_exon_variant	1/2	2
SH3TC2-DT	ENST00000509139.1	n.63T>C		non_coding_transcript_exon_variant	1/3	2
SH3TC2-DT	ENST00000515304.2	n.264T>C		non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73019 AN: 151884 Hom.: 18794 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.498

GnomAD4 exome AF: 0.498 AC: 3933 AN: 7892 Hom.: 1055 Cov.: 0 AF XY: 0.489 AC XY: 2026 AN XY: 4142

Gnomad4 AFR exome AF: 0.256

Gnomad4 AMR exome AF: 0.431

Gnomad4 ASJ exome AF: 0.518

Gnomad4 EAS exome AF: 0.543

Gnomad4 SAS exome AF: 0.319

Gnomad4 FIN exome AF: 0.634

Gnomad4 NFE exome AF: 0.557

Gnomad4 OTH exome AF: 0.525

GnomAD4 genome AF: 0.481 AC: 73039 AN: 152002 Hom.: 18800 Cov.: 32 AF XY: 0.479 AC XY: 35596 AN XY: 74302

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.496

Alfa AF: 0.495 Hom.: 2817

Bravo AF: 0.466

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705960; hg19: chr5-148443080; COSMIC: COSV60462029;