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

Publications

5 publications found

Variant links:

COSMIC-nc: COSV60462029

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	ENST00000512007.2 link	n.231T>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

African (AFR)

AF:

0.256

AC:

AN:

348

American (AMR)

AF:

0.431

AC:

613

AN:

1422

Ashkenazi Jewish (ASJ)

AF:

0.518

AC:

AN:

110

East Asian (EAS)

AF:

0.543

AC:

253

AN:

466

South Asian (SAS)

AF:

0.319

AC:

218

AN:

684

European-Finnish (FIN)

AF:

0.634

AC:

AN:

112

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.557

AC:

2438

AN:

4380

Other (OTH)

AF:

0.525

AC:

188

AN:

358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

188

283

377

471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.481

AC:

73039

AN:

152002

Hom.:

18800

Cov.:

AF XY:

0.479

AC XY:

35596

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.309

AC:

12821

AN:

41440

American (AMR)

AF:

0.475

AC:

7258

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1777

AN:

3472

East Asian (EAS)

AF:

0.545

AC:

2812

AN:

5164

South Asian (SAS)

AF:

0.342

AC:

1647

AN:

4814

European-Finnish (FIN)

AF:

0.619

AC:

6537

AN:

10560

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.567

AC:

38521

AN:

67956

Other (OTH)

AF:

0.496

AC:

1047

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1884

3768

5653

7537

9421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

(source)

DANN

Benign

0.86

PhyloP100

-0.28

PromoterAI

-0.021

Neutral

(source)

Splicing

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

Publications

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5-149063517-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over