Variant chr2-11160606-C-T 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.227-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 1,613,580 control chromosomes in the GnomAD database, including 183,717 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 0.40 ( 13352 hom., cov: 31)

Exomes 𝑓: 0.48 ( 170365 hom. )

Consequence

SLC66A3
NM_152391.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.36

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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC66A3	NM_152391.5 linkuse as main transcript	c.227-19C>T		intron_variant		ENST00000295083.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC66A3	ENST00000295083.8 linkuse as main transcript	c.227-19C>T		intron_variant		1	NM_152391.5	P1	Q8N755-1

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

60270

AN:

151814

Hom.:

13347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.495

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.417

GnomAD3 exomes

AF:

0.454

AC:

114063

AN:

251476

Hom.:

26831

AF XY:

0.462

AC XY:

62746

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.426

Gnomad ASJ exome

AF:

0.425

Gnomad EAS exome

AF:

0.480

Gnomad SAS exome

AF:

0.499

Gnomad FIN exome

AF:

0.424

Gnomad NFE exome

AF:

0.491

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.479

AC:

700033

AN:

1461650

Hom.:

170365

Cov.:

AF XY:

0.480

AC XY:

349276

AN XY:

727144

show subpopulations

Gnomad4 AFR exome

AF:

0.183

Gnomad4 AMR exome

AF:

0.427

Gnomad4 ASJ exome

AF:

0.420

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.498

Gnomad4 FIN exome

AF:

0.427

Gnomad4 NFE exome

AF:

0.493

Gnomad4 OTH exome

AF:

0.466

GnomAD4 genome

AF:

0.397

AC:

60284

AN:

151930

Hom.:

13352

Cov.:

AF XY:

0.396

AC XY:

29410

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.412

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.513

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.491

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.479

Hom.:

29518

Bravo

AF:

0.385

Asia WGS

AF:

0.448

AC:

1561

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.13

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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