rs41318021

Positions:

• chr13-29514470-G-A

Variant summary

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

The NM_003045.5(SLC7A1):​c.*10C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 1,601,734 control chromosomes in the GnomAD database, including 6,737 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 0.063 (457 hom., cov: 33)
  • Exomes 𝑓: 0.087 (6280 hom.)
• Consequence: SLC7A1 NM_003045.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

Genes affected

SLC7A1 (HGNC:11057): (solute carrier family 7 member 1) Enables L-arginine transmembrane transporter activity and L-histidine transmembrane transporter activity. Involved in amino acid transport. Located in membrane. Part of apical plasma membrane; basolateral plasma membrane; and protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A1	NM_003045.5	c.*10C>T		3_prime_UTR_variant	13/13	ENST00000380752.10	NP_003036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A1	ENST00000380752	c.*10C>T		3_prime_UTR_variant	13/13	1	NM_003045.5	ENSP00000370128.5

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9642 AN: 152168 Hom.: 457 Cov.: 33

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.0455

GnomAD3 exomes AF: 0.0661 AC: 16028 AN: 242302 Hom.: 779 AF XY: 0.0672 AC XY: 8872 AN XY: 131974

Gnomad AFR exome AF: 0.0134

Gnomad AMR exome AF: 0.0342

Gnomad ASJ exome AF: 0.0330

Gnomad EAS exome AF: 0.000220

Gnomad SAS exome AF: 0.0337

Gnomad FIN exome AF: 0.143

Gnomad NFE exome AF: 0.0949

Gnomad OTH exome AF: 0.0643

GnomAD4 exome AF: 0.0866 AC: 125456 AN: 1449448 Hom.: 6280 Cov.: 29 AF XY: 0.0848 AC XY: 61184 AN XY: 721530

Gnomad4 AFR exome AF: 0.0116

Gnomad4 AMR exome AF: 0.0336

Gnomad4 ASJ exome AF: 0.0342

Gnomad4 EAS exome AF: 0.000202

Gnomad4 SAS exome AF: 0.0353

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.0982

Gnomad4 OTH exome AF: 0.0723

GnomAD4 genome AF: 0.0633 AC: 9644 AN: 152286 Hom.: 457 Cov.: 33 AF XY: 0.0632 AC XY: 4702 AN XY: 74454

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0746 Hom.: 128

Bravo AF: 0.0540

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	5.9
DANN	Benign	0.86
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs41318021; hg19: chr13-30088607;