rs2848634

chr11-57484855-G-Achr11-57484855-G-Cchr11-57484855-G-T

Variant summary

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

The NM_003627.6(SLC43A1):c.*241C>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 0.76 in 398,836 control chromosomes in the GnomAD database, including 115,771 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 0.75 (43357 hom., cov: 32)
  • Exomes 𝑓: 0.76 (72414 hom.)
• Consequence: SLC43A1 NM_003627.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.32

Genes affected

SLC43A1 (HGNC:9225): (solute carrier family 43 member 1) SLC43A1 belongs to the system L family of plasma membrane carrier proteins that transports large neutral amino acids (Babu et al., 2003 [PubMed 12930836]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC43A1	NM_003627.6	c.*241C>T		3_prime_UTR_variant	15/15	ENST00000278426.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC43A1	ENST00000278426.8	c.*241C>T		3_prime_UTR_variant	15/15	1	NM_003627.6	P1
SLC43A1	ENST00000528450.5	c.*241C>T		3_prime_UTR_variant	15/15	1		P1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114553 AN: 151970 Hom.: 43325 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.766

GnomAD4 exome AF: 0.763 AC: 188363 AN: 246746 Hom.: 72414 Cov.: 4 AF XY: 0.763 AC XY: 97932 AN XY: 128270

Gnomad4 AFR exome AF: 0.710

Gnomad4 AMR exome AF: 0.734

Gnomad4 ASJ exome AF: 0.840

Gnomad4 EAS exome AF: 0.848

Gnomad4 SAS exome AF: 0.765

Gnomad4 FIN exome AF: 0.784

Gnomad4 NFE exome AF: 0.752

Gnomad4 OTH exome AF: 0.767

GnomAD4 genome AF: 0.754 AC: 114626 AN: 152090 Hom.: 43357 Cov.: 32 AF XY: 0.759 AC XY: 56468 AN XY: 74364

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.768

Alfa AF: 0.759 Hom.: 73184

Bravo AF: 0.748

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.3
Dann	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2848634; hg19: chr11-57252328;