Variant 6-127476034-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001400265.1(MTCL3):c.1992C>T(p.Ala664Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 1,611,188 control chromosomes in the GnomAD database, including 68,632 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6698 hom., cov: 32)

Exomes 𝑓: 0.27 ( 61934 hom. )

Consequence

MTCL3
NM_001400265.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

SOGA3 (HGNC:21494): (MTCL family member 3) Predicted to be involved in regulation of autophagy. Predicted to be located in extracellular space. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SOGA3 links:

ENSG00000255330 (HGNC:):

ENSG00000255330 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 6-127476034-G-A is Benign according to our data. Variant chr6-127476034-G-A is described in ClinVar as [Benign]. Clinvar id is 1329644.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.15 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTCL3	NM_001400265.1 linkuse as main transcript	c.1992C>T	p.Ala664Ala	synonymous_variant	6/7		NP_001387194.1
SOGA3-KIAA0408	NR_174482.1 linkuse as main transcript	n.2837C>T		non_coding_transcript_exon_variant	6/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOGA3	ENST00000525778.6 linkuse as main transcript	c.1992C>T	p.Ala664Ala	synonymous_variant	6/7	5		ENSP00000434570.1		Q5TF21
ENSG00000255330	ENST00000481848.6 linkuse as main transcript	n.1992C>T		non_coding_transcript_exon_variant	6/12	5		ENSP00000455908.1

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41770

AN:

151816

Hom.:

6690

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.339

AC:

83947

AN:

247782

Hom.:

17409

AF XY:

0.328

AC XY:

44094

AN XY:

134566

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.555

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.718

Gnomad SAS exome

AF:

0.315

Gnomad FIN exome

AF:

0.317

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.274

AC:

399546

AN:

1459254

Hom.:

61934

Cov.:

AF XY:

0.273

AC XY:

198391

AN XY:

726034

show subpopulations

Gnomad4 AFR exome

AF:

0.206

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.197

Gnomad4 EAS exome

AF:

0.724

Gnomad4 SAS exome

AF:

0.317

Gnomad4 FIN exome

AF:

0.311

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.276

GnomAD4 genome

AF:

0.275

AC:

41811

AN:

151934

Hom.:

6698

Cov.:

AF XY:

0.282

AC XY:

20935

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.713

Gnomad4 SAS

AF:

0.318

Gnomad4 FIN

AF:

0.307

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.263

Alfa

AF:

0.250

Hom.:

8363

Bravo

AF:

0.284

Asia WGS

AF:

0.490

AC:

1702

AN:

3478

EpiCase

AF:

0.241

EpiControl

AF:

0.246

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

5.1

DANN

Benign

0.92

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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