Variant 3-126007205-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_017836.4(SLC41A3):c.1275C>G(p.Leu425Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 1,613,690 control chromosomes in the GnomAD database, including 320,514 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 36897 hom., cov: 32)

Exomes 𝑓: 0.62 ( 283617 hom. )

Consequence

SLC41A3
NM_017836.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.359

Variant links:

Genes affected

SLC41A3 (HGNC:31046): (solute carrier family 41 member 3) Predicted to enable cation transmembrane transporter activity. Predicted to be involved in cation transmembrane transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC41A3 links:

SLC41A3 (HGNC:):

SLC41A3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 3-126007205-G-C is Benign according to our data. Variant chr3-126007205-G-C is described in ClinVar as [Benign]. Clinvar id is 1253374.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.359 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A3	NM_017836.4 linkuse as main transcript	c.1275C>G	p.Leu425Leu	synonymous_variant	11/11	ENST00000360370.9	NP_060306.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A3	ENST00000360370.9 linkuse as main transcript	c.1275C>G	p.Leu425Leu	synonymous_variant	11/11	1	NM_017836.4	ENSP00000353533.4		Q96GZ6-9

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103620

AN:

152030

Hom.:

36842

Cov.:

show subpopulations

Gnomad AFR

AF:

0.896

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.567

Gnomad ASJ

AF:

0.730

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.619

Gnomad OTH

AF:

0.715

GnomAD3 exomes

AF:

0.594

AC:

147324

AN:

247942

Hom.:

45602

AF XY:

0.598

AC XY:

80207

AN XY:

134224

show subpopulations

Gnomad AFR exome

AF:

0.901

Gnomad AMR exome

AF:

0.427

Gnomad ASJ exome

AF:

0.735

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.583

Gnomad FIN exome

AF:

0.525

Gnomad NFE exome

AF:

0.623

Gnomad OTH exome

AF:

0.624

GnomAD4 exome

AF:

0.619

AC:

904714

AN:

1461542

Hom.:

283617

Cov.:

AF XY:

0.619

AC XY:

450118

AN XY:

727054

show subpopulations

Gnomad4 AFR exome

AF:

0.909

Gnomad4 AMR exome

AF:

0.442

Gnomad4 ASJ exome

AF:

0.731

Gnomad4 EAS exome

AF:

0.532

Gnomad4 SAS exome

AF:

0.586

Gnomad4 FIN exome

AF:

0.530

Gnomad4 NFE exome

AF:

0.623

Gnomad4 OTH exome

AF:

0.641

GnomAD4 genome

AF:

0.682

AC:

103733

AN:

152148

Hom.:

36897

Cov.:

AF XY:

0.673

AC XY:

50035

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.897

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.730

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.601

Gnomad4 FIN

AF:

0.528

Gnomad4 NFE

AF:

0.619

Gnomad4 OTH

AF:

0.717

Alfa

AF:

0.610

Hom.:

7506

Bravo

AF:

0.692

Asia WGS

AF:

0.610

AC:

2119

AN:

3478

EpiCase

AF:

0.642

EpiControl

AF:

0.656

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

4.4

DANN

Benign

0.73

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