Variant 8-103401307-T-TC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000297578.9(SLC25A32):c.812+208_812+209insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,142 control chromosomes in the GnomAD database, including 4,027 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4027 hom., cov: 27)

Consequence

SLC25A32
ENST00000297578.9 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.11

Variant links:

Genes affected

SLC25A32 (HGNC:29683): (solute carrier family 25 member 32) This gene encodes a member of the P(I/L)W subfamily of mitochondrial carrier family transport proteins. The encoded protein transports folate across the inner mitochondrial membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2013]

SLC25A32 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-103401307-T-TC is Benign according to our data. Variant chr8-103401307-T-TC is described in ClinVar as [Benign]. Clinvar id is 1238386.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SLC25A32	NM_030780.5 linkuse as main transcript	c.812+208_812+209insG	intron_variant	ENST00000297578.9	NP_110407.2
SLC25A32	NR_102337.2 linkuse as main transcript	n.896+208_896+209insG	intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2 linkuse as main transcript	n.1091+208_1091+209insG	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A32	ENST00000297578.9 linkuse as main transcript	c.812+208_812+209insG		intron_variant		1	NM_030780.5	ENSP00000297578	P1

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34486

AN:

152024

Hom.:

4016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.229

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.227

AC:

34521

AN:

152142

Hom.:

4027

Cov.:

AF XY:

0.231

AC XY:

17201

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.210

Hom.:

427

Bravo

AF:

0.224

Asia WGS

AF:

0.305

AC:

1059

AN:

3478

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

Aug 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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