chr1-205795305-A-C
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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
NM_173854.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.423
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]
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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 |
---|---|---|---|---|---|---|---|
SLC41A1 | NM_173854.6 | c.1207+39T>G | intron_variant | ENST00000367137.4 | |||
SLC41A1 | XM_047416887.1 | c.1207+39T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC41A1 | ENST00000367137.4 | c.1207+39T>G | intron_variant | 1 | NM_173854.6 | P1 | |||
SLC41A1 | ENST00000468057.5 | n.1003+39T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
SLC41A1 | ENST00000484228.1 | n.1273+39T>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0318 AC: 4826AN: 151772Hom.: 115 Cov.: 32
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GnomAD3 exomes AF: 0.0364 AC: 9124AN: 250392Hom.: 228 AF XY: 0.0384 AC XY: 5203AN XY: 135344
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GnomAD4 exome AF: 0.0429 AC: 62772AN: 1461602Hom.: 1488 Cov.: 33 AF XY: 0.0434 AC XY: 31534AN XY: 727068
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GnomAD4 genome AF: 0.0317 AC: 4821AN: 151890Hom.: 114 Cov.: 32 AF XY: 0.0321 AC XY: 2384AN XY: 74236
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at