Variant 1-205795305-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173854.6(SLC41A1):c.1207+39T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 1,613,492 control chromosomes in the GnomAD database, including 1,602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.032 ( 114 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1488 hom. )

Consequence

SLC41A1
NM_173854.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.423

Variant links:

Genes affected

SLC41A1 (HGNC:19429): (solute carrier family 41 member 1) Enables magnesium ion transmembrane transporter activity and magnesium:sodium antiporter activity. Involved in cellular magnesium ion homeostasis; cellular response to magnesium ion; and magnesium ion transmembrane transport. Located in basolateral plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

SLC41A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-205795305-A-C is Benign according to our data. Variant chr1-205795305-A-C is described in ClinVar as [Benign]. Clinvar id is 1270504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.054 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A1	NM_173854.6 linkuse as main transcript	c.1207+39T>G		intron_variant		ENST00000367137.4	NP_776253.3
SLC41A1	XM_047416887.1 linkuse as main transcript	c.1207+39T>G		intron_variant			XP_047272843.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
SLC41A1	ENST00000367137.4 linkuse as main transcript	c.1207+39T>G	intron_variant	1	NM_173854.6	ENSP00000356105	P1
SLC41A1	ENST00000468057.5 linkuse as main transcript	n.1003+39T>G	intron_variant, non_coding_transcript_variant	2
SLC41A1	ENST00000484228.1 linkuse as main transcript	n.1273+39T>G	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0318

AC:

4826

AN:

151772

Hom.:

115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0125

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.00271

Gnomad SAS

AF:

0.0509

Gnomad FIN

AF:

0.0528

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0433

Gnomad OTH

AF:

0.0321

GnomAD3 exomes

AF:

0.0364

AC:

9124

AN:

250392

Hom.:

228

AF XY:

0.0384

AC XY:

5203

AN XY:

135344

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.0190

Gnomad ASJ exome

AF:

0.0253

Gnomad EAS exome

AF:

0.00147

Gnomad SAS exome

AF:

0.0532

Gnomad FIN exome

AF:

0.0524

Gnomad NFE exome

AF:

0.0446

Gnomad OTH exome

AF:

0.0334

GnomAD4 exome

AF:

0.0429

AC:

62772

AN:

1461602

Hom.:

1488

Cov.:

AF XY:

0.0434

AC XY:

31534

AN XY:

727068

show subpopulations

Gnomad4 AFR exome

AF:

0.0117

Gnomad4 AMR exome

AF:

0.0197

Gnomad4 ASJ exome

AF:

0.0250

Gnomad4 EAS exome

AF:

0.000831

Gnomad4 SAS exome

AF:

0.0554

Gnomad4 FIN exome

AF:

0.0503

Gnomad4 NFE exome

AF:

0.0456

Gnomad4 OTH exome

AF:

0.0389

GnomAD4 genome

AF:

0.0317

AC:

4821

AN:

151890

Hom.:

114

Cov.:

AF XY:

0.0321

AC XY:

2384

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.0125

Gnomad4 AMR

AF:

0.0222

Gnomad4 ASJ

AF:

0.0242

Gnomad4 EAS

AF:

0.00271

Gnomad4 SAS

AF:

0.0505

Gnomad4 FIN

AF:

0.0528

Gnomad4 NFE

AF:

0.0433

Gnomad4 OTH

AF:

0.0318

Alfa

AF:

0.0360

Hom.:

Bravo

AF:

0.0282

Asia WGS

AF:

0.0250

AC:

AN:

3478

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	clinical testing	GeneDx	May 17, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.4

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