chr1-205795305-A-C

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

2

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]

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 UniProt
SLC41A1NM_173854.6 linkuse as main transcriptc.1207+39T>G intron_variant ENST00000367137.4
SLC41A1XM_047416887.1 linkuse as main transcriptc.1207+39T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC41A1ENST00000367137.4 linkuse as main transcriptc.1207+39T>G intron_variant 1 NM_173854.6 P1
SLC41A1ENST00000468057.5 linkuse as main transcriptn.1003+39T>G intron_variant, non_coding_transcript_variant 2
SLC41A1ENST00000484228.1 linkuse as main transcriptn.1273+39T>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0318
AC:
4826
AN:
151772
Hom.:
115
Cov.:
32
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.:
33
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.:
32
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.:
28
Bravo
AF:
0.0282
Asia WGS
AF:
0.0250
AC:
87
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 submitterclinical testingGeneDxMay 17, 2021- -
Benign, criteria provided, single submitternot providedBreakthrough 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.

Other links and lift over

dbSNP: rs56052552; hg19: chr1-205764433; API