Variant 15-79899104-G-GA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001199760.2(ST20-MTHFS):c.45+8524_45+8525insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 152,262 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0024 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

ST20-MTHFS
NM_001199760.2 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.414

Variant links:

Genes affected

ST20-MTHFS (HGNC:44655): (ST20-MTHFS readthrough) This locus represents naturally occurring read-through transcription between the neighboring suppressor of tumorigenicity 20 and 5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase) genes on chromosome 15. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Dec 2010]

ST20-MTHFS links:

ST20 (HGNC:):

ST20 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 15-79899104-G-GA is Benign according to our data. Variant chr15-79899104-G-GA is described in ClinVar as [Likely_benign]. Clinvar id is 733522.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein	UniProt
ST20-MTHFS	NM_001199760.2 linkuse as main transcript	c.45+8524_45+8525insT	intron_variant		NP_001186689.1	A0A0A6YYL1
ST20	NR_037652.2 linkuse as main transcript	n.378_379insT	non_coding_transcript_exon_variant	3/3
ST20	NR_037653.2 linkuse as main transcript	n.400_401insT	non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST20-MTHFS	ENST00000479961.1 linkuse as main transcript	c.45+8524_45+8525insT		intron_variant		3		ENSP00000455643.1		A0A0A6YYL1

Frequencies

GnomAD3 genomes

AF:

0.00152

AC:

232

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000720

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.000472

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00262

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00168

AC:

421

AN:

250902

Hom.:

AF XY:

0.00171

AC XY:

232

AN XY:

135698

show subpopulations

Gnomad AFR exome

AF:

0.000124

Gnomad AMR exome

AF:

0.000378

Gnomad ASJ exome

AF:

0.000894

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00141

Gnomad FIN exome

AF:

0.000462

Gnomad NFE exome

AF:

0.00295

Gnomad OTH exome

AF:

0.00148

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00236

AC:

3442

AN:

1461404

Hom.:

Cov.:

AF XY:

0.00225

AC XY:

1638

AN XY:

727000

show subpopulations

Gnomad4 AFR exome

AF:

0.000209

Gnomad4 AMR exome

AF:

0.000515

Gnomad4 ASJ exome

AF:

0.000651

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00143

Gnomad4 FIN exome

AF:

0.000356

Gnomad4 NFE exome

AF:

0.00286

Gnomad4 OTH exome

AF:

0.00123

GnomAD4 genome

AF:

0.00152

AC:

231

AN:

152262

Hom.:

Cov.:

AF XY:

0.00121

AC XY:

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.000719

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.000472

Gnomad4 NFE

AF:

0.00262

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00192

Hom.:

Bravo

AF:

0.00153

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00295

EpiControl

AF:

0.00267

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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