3-126033450-A-G

Variant names:

• chr3-126033450-A-G
• rs11716991
• NM_017836.4:c.453+157T>C

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.453+157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,978 control chromosomes in the GnomAD database, including 1,640 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.14 (1640 hom., cov: 32)
• Consequence: SLC41A3 NM_017836.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.272
• Publications: 3 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 3-126033450-A-G is Benign according to our data. Variant chr3-126033450-A-G is described in ClinVar as Benign. ClinVar VariationId is 1270595.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A3	NM_017836.4	c.453+157T>C		intron_variant	Intron 4 of 10	ENST00000360370.9	NP_060306.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A3	ENST00000360370.9	c.453+157T>C		intron_variant	Intron 4 of 10	1	NM_017836.4	ENSP00000353533.4

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21091 AN: 151860 Hom.: 1636 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.139 AC: 21116 AN: 151978 Hom.: 1640 Cov.: 32 AF XY: 0.134 AC XY: 9983 AN XY: 74278

African (AFR) AF: 0.179 AC: 7407 AN: 41434

American (AMR) AF: 0.113 AC: 1721 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.0207 AC: 106 AN: 5130

South Asian (SAS) AF: 0.0727 AC: 349 AN: 4802

European-Finnish (FIN) AF: 0.0944 AC: 1000 AN: 10594

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9410 AN: 67958

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.121 Hom.: 693

Bravo AF: 0.140

Asia WGS AF: 0.0590 AC: 204 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	-0.89
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.27
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: rs11716991; hg19: chr3-125752293;