Variant chr5-149071352-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000515519.6(SH3TC2-DT):n.608C>G 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 0.498 in 152,050 control chromosomes in the GnomAD database, including 20,237 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 0.50 ( 20233 hom., cov: 32)

Exomes 𝑓: 0.42 ( 4 hom. )

Consequence

SH3TC2-DT
ENST00000515519.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.713

Variant links:

Genes affected

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

SH3TC2-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3TC2-DT	NR_122044.1 link	n.467+6994C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
SH3TC2-DT	ENST00000515519.6 link	n.608C>G	non_coding_transcript_exon_variant	4/4	5
SH3TC2-DT	ENST00000507373.1 link	n.66+7678C>G	intron_variant		5
SH3TC2-DT	ENST00000509139.1 link	n.329+6994C>G	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75589

AN:

151894

Hom.:

20186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.483

GnomAD4 exome

AF:

0.421

AC:

AN:

Hom.:

Cov.:

AF XY:

0.375

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.375

Gnomad4 NFE exome

AF:

0.462

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.498

AC:

75690

AN:

152012

Hom.:

20233

Cov.:

AF XY:

0.502

AC XY:

37293

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.684

Gnomad4 AMR

AF:

0.507

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.456

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.370

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.287

Hom.:

707

Bravo

AF:

0.512

Asia WGS

AF:

0.539

AC:

1876

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.70

DANN

Benign

0.38

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over