chr5-1444312-T-G

Variant names:

• chr5-1444312-T-G
• rs2963238
• NM_001044.5:c.-46+1036A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001044.5(SLC6A3):​c.-46+1036A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,916 control chromosomes in the GnomAD database, including 20,312 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 0.50 (20312 hom., cov: 32)
• Consequence: SLC6A3 NM_001044.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 14 publications found

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 Gene-Disease associations (from GenCC):

• classic dopamine transporter deficiency syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• SLC6A3-related dopamine transporter deficiency syndrome

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• parkinsonism-dystonia, infantile

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A3	NM_001044.5	c.-46+1036A>C		intron_variant	Intron 1 of 14	ENST00000270349.12	NP_001035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A3	ENST00000270349.12	c.-46+1036A>C		intron_variant	Intron 1 of 14	1	NM_001044.5	ENSP00000270349.9
SLC6A3	ENST00000713696.1	c.-46+1036A>C		intron_variant	Intron 1 of 14			ENSP00000519000.1
SLC6A3	ENST00000713698.1	c.-46+1036A>C		intron_variant	Intron 1 of 4			ENSP00000519002.1
SLC6A3	ENST00000713697.1	n.-46+1036A>C		intron_variant	Intron 1 of 10			ENSP00000519001.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76320 AN: 151798 Hom.: 20293 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.503 AC: 76387 AN: 151916 Hom.: 20312 Cov.: 32 AF XY: 0.502 AC XY: 37235 AN XY: 74230

African (AFR) AF: 0.364 AC: 15066 AN: 41382

American (AMR) AF: 0.479 AC: 7319 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3468

East Asian (EAS) AF: 0.165 AC: 850 AN: 5160

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4818

European-Finnish (FIN) AF: 0.570 AC: 6010 AN: 10540

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.601 AC: 40873 AN: 67970

Other (OTH) AF: 0.521 AC: 1098 AN: 2108

Alfa AF: 0.555 Hom.: 15523

Bravo AF: 0.485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.56
PhyloP100		0.23
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: rs2963238; hg19: chr5-1444427;