3-126012318-C-T

Variant names:

• chr3-126012318-C-T
• rs1566715
• NM_017836.4:c.1105+297G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_017836.4(SLC41A3):​c.1105+297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,138 control chromosomes in the GnomAD database, including 39,339 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.70 (39339 hom., cov: 33)
• Consequence: SLC41A3 NM_017836.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.117

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]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 3-126012318-C-T is Benign according to our data. Variant chr3-126012318-C-T is described in ClinVar as [Benign]. Clinvar id is 1275158.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A3	NM_017836.4	c.1105+297G>A		intron_variant	Intron 9 of 10	ENST00000360370.9	NP_060306.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A3	ENST00000360370.9	c.1105+297G>A		intron_variant	Intron 9 of 10	1	NM_017836.4	ENSP00000353533.4

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106935 AN: 152020 Hom.: 39282 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.704 AC: 107048 AN: 152138 Hom.: 39339 Cov.: 33 AF XY: 0.694 AC XY: 51626 AN XY: 74338

African (AFR) AF: 0.923 AC: 38342 AN: 41546

American (AMR) AF: 0.579 AC: 8844 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2782 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2556 AN: 5170

South Asian (SAS) AF: 0.649 AC: 3131 AN: 4826

European-Finnish (FIN) AF: 0.534 AC: 5632 AN: 10548

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43441 AN: 67974

Other (OTH) AF: 0.744 AC: 1569 AN: 2110

Alfa AF: 0.667 Hom.: 17572

Bravo AF: 0.714

Asia WGS AF: 0.631 AC: 2192 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.97
DANN	Benign	0.53
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs1566715; hg19: chr3-125731161;