Variant 5-1400883-CGA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001044.5(SLC6A3):c.1839+30_1839+31del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 1,518,040 control chromosomes in the GnomAD database, including 287 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.012 ( 24 hom., cov: 33)

Exomes 𝑓: 0.017 ( 263 hom. )

Consequence

SLC6A3
NM_001044.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.786

Variant links:

Genes affected

SLC6A3 (HGNC:11049): (solute carrier family 6 member 3) This gene encodes a dopamine transporter which is a member of the sodium- and chloride-dependent neurotransmitter transporter family. The 3' UTR of this gene contains a 40 bp tandem repeat, referred to as a variable number tandem repeat or VNTR, which can be present in 3 to 11 copies. Variation in the number of repeats is associated with idiopathic epilepsy, attention-deficit hyperactivity disorder, dependence on alcohol and cocaine, susceptibility to Parkinson disease and protection against nicotine dependence.[provided by RefSeq, Nov 2009]

SLC6A3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-1400883-CGA-C is Benign according to our data. Variant chr5-1400883-CGA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1207981.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0124 (1895/152278) while in subpopulation SAS AF= 0.0223 (107/4806). AF 95% confidence interval is 0.0188. There are 24 homozygotes in gnomad4. There are 903 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A3	NM_001044.5 linkuse as main transcript	c.1839+30_1839+31del		intron_variant		ENST00000270349.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A3	ENST00000270349.12 linkuse as main transcript	c.1839+30_1839+31del		intron_variant		1	NM_001044.5	P1
SLC6A3	ENST00000512002.2 linkuse as main transcript	n.220+30_220+31del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0125

AC:

1895

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00290

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00975

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0222

Gnomad FIN

AF:

0.0177

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0147

AC:

2541

AN:

172698

Hom.:

AF XY:

0.0159

AC XY:

1459

AN XY:

91842

show subpopulations

Gnomad AFR exome

AF:

0.00332

Gnomad AMR exome

AF:

0.00572

Gnomad ASJ exome

AF:

0.0128

Gnomad EAS exome

AF:

0.000157

Gnomad SAS exome

AF:

0.0227

Gnomad FIN exome

AF:

0.0190

Gnomad NFE exome

AF:

0.0190

Gnomad OTH exome

AF:

0.0140

GnomAD4 exome

AF:

0.0170

AC:

23189

AN:

1365762

Hom.:

263

AF XY:

0.0176

AC XY:

11942

AN XY:

677544

show subpopulations

Gnomad4 AFR exome

AF:

0.00311

Gnomad4 AMR exome

AF:

0.00656

Gnomad4 ASJ exome

AF:

0.0136

Gnomad4 EAS exome

AF:

0.000110

Gnomad4 SAS exome

AF:

0.0233

Gnomad4 FIN exome

AF:

0.0176

Gnomad4 NFE exome

AF:

0.0180

Gnomad4 OTH exome

AF:

0.0154

GnomAD4 genome

AF:

0.0124

AC:

1895

AN:

152278

Hom.:

Cov.:

AF XY:

0.0121

AC XY:

903

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.00974

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0223

Gnomad4 FIN

AF:

0.0177

Gnomad4 NFE

AF:

0.0185

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.0171

Hom.:

Bravo

AF:

0.0115

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over