19-46784682-T-C

Position:

• chr19-46784682-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005628.3(SLC1A5):​c.567-123A>G 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 1,595,402 control chromosomes in the GnomAD database, including 91,900 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 0.33 (8586 hom., cov: 32)
  • Exomes 𝑓: 0.34 (83314 hom.)
• Consequence: SLC1A5 NM_005628.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

SLC1A5 (HGNC:10943): (solute carrier family 1 member 5) The SLC1A5 gene encodes a sodium-dependent neutral amino acid transporter that can act as a receptor for RD114/type D retrovirus (Larriba et al., 2001 [PubMed 11781704]).[supplied by OMIM, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A5	NM_005628.3	c.567-123A>G		intron_variant		ENST00000542575.6
SLC1A5	NM_001145145.2	c.-85A>G		5_prime_UTR_variant	1/7
SLC1A5	NM_001145144.2	c.-118-123A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A5	ENST00000542575.6	c.567-123A>G		intron_variant		1	NM_005628.3	P1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50718 AN: 151872 Hom.: 8580 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.301

GnomAD3 exomes AF: 0.333 AC: 72403 AN: 217328 Hom.: 11896 AF XY: 0.336 AC XY: 39734 AN XY: 118166

Gnomad AFR exome AF: 0.339

Gnomad AMR exome AF: 0.289

Gnomad ASJ exome AF: 0.344

Gnomad EAS exome AF: 0.242

Gnomad SAS exome AF: 0.340

Gnomad FIN exome AF: 0.380

Gnomad NFE exome AF: 0.350

Gnomad OTH exome AF: 0.327

GnomAD4 exome AF: 0.339 AC: 489243 AN: 1443412 Hom.: 83314 Cov.: 34 AF XY: 0.339 AC XY: 243221 AN XY: 716752

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.283

Gnomad4 ASJ exome AF: 0.340

Gnomad4 EAS exome AF: 0.266

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.382

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.322

GnomAD4 genome AF: 0.334 AC: 50744 AN: 151990 Hom.: 8586 Cov.: 32 AF XY: 0.331 AC XY: 24576 AN XY: 74262

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.301

Alfa AF: 0.335 Hom.: 10899

Bravo AF: 0.325

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.66

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: rs313853; hg19: chr19-47287939; COSMIC: COSV69466742; COSMIC: COSV69466742;