rs7617162

Variant names:

• chr3-126036607-C-T
• rs7617162
• NM_017836.4:c.382-2929G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017836.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A3	NM_017836.4	MANE Select	c.382-2929G>A		intron	N/A	NP_060306.4
	SLC41A3	NM_001008485.2		c.382-2929G>A		intron	N/A	NP_001008485.2
	SLC41A3	NM_001008486.2		c.274-2929G>A		intron	N/A	NP_001008486.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A3	ENST00000360370.9	TSL:1 MANE Select	c.382-2929G>A		intron	N/A	ENSP00000353533.4
	SLC41A3	ENST00000315891.10	TSL:1	c.382-2929G>A		intron	N/A	ENSP00000326070.6
	SLC41A3	ENST00000514677.5	TSL:1	c.427-2929G>A		intron	N/A	ENSP00000422828.1

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

African (AFR) AF: 0.357 AC: 14770 AN: 41416

American (AMR) AF: 0.290 AC: 4423 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1529 AN: 5140

South Asian (SAS) AF: 0.335 AC: 1607 AN: 4792

European-Finnish (FIN) AF: 0.218 AC: 2299 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23373 AN: 67908

Other (OTH) AF: 0.365 AC: 767 AN: 2100

Alfa AF: 0.327 Hom.: 1067

Bravo AF: 0.337

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.56
PhyloP100		-2.7
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

Other links and lift over

dbSNP: rs7617162; hg19: chr3-125755450;