Variant rs3732103 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152391.5(SLC66A3):c.475+53C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 1,584,898 control chromosomes in the GnomAD database, including 236,812 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 0.51 ( 19976 hom., cov: 31)

Exomes 𝑓: 0.55 ( 216836 hom. )

Consequence

SLC66A3
NM_152391.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

Variant links:

Genes affected

SLC66A3 (HGNC:28503): (solute carrier family 66 member 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC66A3 links:

SLC66A3 (HGNC:):

SLC66A3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC66A3	NM_152391.5 linkuse as main transcript	c.475+53C>T		intron_variant		ENST00000295083.8	NP_689604.1	Q8N755-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC66A3	ENST00000295083.8 linkuse as main transcript	c.475+53C>T		intron_variant		1	NM_152391.5	ENSP00000295083.3		Q8N755-1

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77229

AN:

151650

Hom.:

19960

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.587

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.524

GnomAD4 exome

AF:

0.548

AC:

785376

AN:

1433128

Hom.:

216836

AF XY:

0.549

AC XY:

391856

AN XY:

714088

show subpopulations

Gnomad4 AFR exome

AF:

0.418

Gnomad4 AMR exome

AF:

0.478

Gnomad4 ASJ exome

AF:

0.591

Gnomad4 EAS exome

AF:

0.460

Gnomad4 SAS exome

AF:

0.531

Gnomad4 FIN exome

AF:

0.485

Gnomad4 NFE exome

AF:

0.561

Gnomad4 OTH exome

AF:

0.542

GnomAD4 genome

AF:

0.509

AC:

77291

AN:

151770

Hom.:

19976

Cov.:

AF XY:

0.505

AC XY:

37430

AN XY:

74128

show subpopulations

Gnomad4 AFR

AF:

0.425

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.587

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.477

Gnomad4 NFE

AF:

0.562

Gnomad4 OTH

AF:

0.523

Alfa

AF:

0.551

Hom.:

12356

Bravo

AF:

0.507

Asia WGS

AF:

0.467

AC:

1626

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.5

DANN

Benign

0.46

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over