rs3819252

chr11-20627858-G-Achr11-20627858-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004211.5(SLC6A5):c.1396-122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 739,806 control chromosomes in the GnomAD database, including 43,499 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8133 hom., cov: 31)
  • Exomes 𝑓: 0.34 (35366 hom.)
• Consequence: SLC6A5 NM_004211.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.07

Genes affected

SLC6A5 (HGNC:11051): (solute carrier family 6 member 5) This gene encodes a sodium- and chloride-dependent glycine neurotransmitter transporter. This integral membrane glycoprotein is responsible for the clearance of extracellular glycine during glycine-mediated neurotransmission. This protein is found in glycinergic axons and maintains a high presynaptic pool of neurotransmitter at glycinergic synapses. Mutations in this gene cause hyperekplexia; a heterogenous neurological disorder characterized by exaggerated startle responses and neonatal apnea. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-20627858-G-A is Benign according to our data. Variant chr11-20627858-G-A is described in ClinVar as [Benign]. Clinvar id is 1228502.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A5	NM_004211.5	c.1396-122G>A		intron_variant		ENST00000525748.6
SLC6A5	NM_001318369.2	c.694-122G>A		intron_variant
SLC6A5	XM_017018544.3	c.520-122G>A		intron_variant
SLC6A5	XR_007062528.1	n.774-122G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A5	ENST00000525748.6	c.1396-122G>A		intron_variant		1	NM_004211.5	P1
SLC6A5	ENST00000298923.11	c.*693-122G>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48527 AN: 151730 Hom.: 8130 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.343 AC: 201467 AN: 587958 Hom.: 35366 AF XY: 0.341 AC XY: 108457 AN XY: 318240

Gnomad4 AFR exome AF: 0.235

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.255

Gnomad4 FIN exome AF: 0.343

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.354

GnomAD4 genome AF: 0.320 AC: 48536 AN: 151848 Hom.: 8133 Cov.: 31 AF XY: 0.319 AC XY: 23639 AN XY: 74190

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.347

Alfa AF: 0.357 Hom.: 18678

Bravo AF: 0.314

Asia WGS AF: 0.269 AC: 939 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.66
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs3819252; hg19: chr11-20649404; COSMIC: COSV54234435; COSMIC: COSV54234435;