3-126006809-C-T

Position:

• chr3-126006809-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_017836.4(SLC41A3):​c.*207G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 1,445,314 control chromosomes in the GnomAD database, including 3,323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.056 (289 hom., cov: 33)
  • Exomes 𝑓: 0.065 (3034 hom.)
• Consequence: SLC41A3 NM_017836.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.222

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]

SLC41A3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 3-126006809-C-T is Benign according to our data. Variant chr3-126006809-C-T is described in ClinVar as [Benign]. Clinvar id is 1288070.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A3	NM_017836.4	c.*207G>A		3_prime_UTR_variant	11/11	ENST00000360370.9	NP_060306.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A3	ENST00000360370.9	c.*207G>A		3_prime_UTR_variant	11/11	1	NM_017836.4	ENSP00000353533.4

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8565 AN: 152224 Hom.: 289 Cov.: 33

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0655 AC: 84648 AN: 1292972 Hom.: 3034 Cov.: 34 AF XY: 0.0649 AC XY: 40763 AN XY: 628472

Gnomad4 AFR exome AF: 0.0455

Gnomad4 AMR exome AF: 0.0386

Gnomad4 ASJ exome AF: 0.102

Gnomad4 EAS exome AF: 0.0000569

Gnomad4 SAS exome AF: 0.0412

Gnomad4 FIN exome AF: 0.0511

Gnomad4 NFE exome AF: 0.0701

Gnomad4 OTH exome AF: 0.0612

GnomAD4 genome AF: 0.0562 AC: 8563 AN: 152342 Hom.: 289 Cov.: 33 AF XY: 0.0536 AC XY: 3994 AN XY: 74498

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0679 Hom.: 498

Bravo AF: 0.0551

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.59

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: rs1044176; hg19: chr3-125725652;