rs7617162

Positions:

• chr3-126036607-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017836.4(SLC41A3):​c.382-2929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,860 control chromosomes in the GnomAD database, including 8,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8653 hom., cov: 31)
• Consequence: SLC41A3 NM_017836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A3	NM_017836.4	c.382-2929G>A		intron_variant		ENST00000360370.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A3	ENST00000360370.9	c.382-2929G>A		intron_variant		1	NM_017836.4	P2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50590 AN: 151744 Hom.: 8642 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.333 AC: 50630 AN: 151860 Hom.: 8653 Cov.: 31 AF XY: 0.326 AC XY: 24184 AN XY: 74214

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.365

Alfa AF: 0.325 Hom.: 1013

Bravo AF: 0.337

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.56

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

Other links and lift over

dbSNP: rs7617162; hg19: chr3-125755450;