Genetic Variant SH3TC2-DT:n.15T>C (chr5-149063517-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000507318.1(SH3TC2-DT):n.15T>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
ENST00000507318.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.279

Variant links:

Genes affected

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

SH3TC2-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SH3TC2-DT	NR_122044.1 link	n.201T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SH3TC2-DT	ENST00000507318.1 link	n.15T>C	non_coding_transcript_exon_variant	Exon 1 of 2	2
SH3TC2-DT	ENST00000509139.1 link	n.63T>C	non_coding_transcript_exon_variant	Exon 1 of 3	2
SH3TC2-DT	ENST00000515304.2 link	n.264T>C	non_coding_transcript_exon_variant	Exon 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73019

AN:

151884

Hom.:

18794

Cov.:

show subpopulations

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.:

AF XY:

0.489

AC XY:

2026

AN XY:

4142

show subpopulations

Gnomad4 AFR exome

AF:

0.256

AC:

AN:

348

Gnomad4 AMR exome

AF:

0.431

AC:

613

AN:

1422

Gnomad4 ASJ exome

AF:

0.518

AC:

AN:

110

Gnomad4 EAS exome

AF:

0.543

AC:

253

AN:

466

Gnomad4 SAS exome

AF:

0.319

AC:

218

AN:

684

Gnomad4 FIN exome

AF:

0.634

AC:

AN:

112

Gnomad4 NFE exome

AF:

0.557

AC:

2438

AN:

4380

Gnomad4 Remaining exome

AF:

0.525

AC:

188

AN:

358

Heterozygous variant carriers

188

283

377

471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

144

192

240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.481

AC:

73039

AN:

152002

Hom.:

18800

Cov.:

AF XY:

0.479

AC XY:

35596

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.309

AC:

0.309387

AN:

0.309387

Gnomad4 AMR

AF:

0.475

AC:

0.475

AN:

0.475

Gnomad4 ASJ

AF:

0.512

AC:

0.511809

AN:

0.511809

Gnomad4 EAS

AF:

0.545

AC:

0.544539

AN:

0.544539

Gnomad4 SAS

AF:

0.342

AC:

0.342127

AN:

0.342127

Gnomad4 FIN

AF:

0.619

AC:

0.619034

AN:

0.619034

Gnomad4 NFE

AF:

0.567

AC:

0.566852

AN:

0.566852

Gnomad4 OTH

AF:

0.496

AC:

0.496209

AN:

0.496209

Heterozygous variant carriers

1884

3768

5653

7537

9421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.490

Hom.:

2864

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 19, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over