chr11-57484855-G-A

Variant names:

• chr11-57484855-G-A
• rs2848634
• NM_003627.6:c.*241C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC43A1	NM_003627.6	c.*241C>T		3_prime_UTR_variant	Exon 15 of 15	ENST00000278426.8	NP_003618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC43A1	ENST00000278426.8	c.*241C>T		3_prime_UTR_variant	Exon 15 of 15	1	NM_003627.6	ENSP00000278426.3
SLC43A1	ENST00000528450.5	c.*241C>T		3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000435673.1

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

African (AFR) AF: 0.710 AC: 5233 AN: 7374

American (AMR) AF: 0.734 AC: 5964 AN: 8122

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 6833 AN: 8130

East Asian (EAS) AF: 0.848 AC: 14069 AN: 16590

South Asian (SAS) AF: 0.765 AC: 14903 AN: 19486

European-Finnish (FIN) AF: 0.784 AC: 11166 AN: 14236

Middle Eastern (MID) AF: 0.765 AC: 866 AN: 1132

European-Non Finnish (NFE) AF: 0.752 AC: 118108 AN: 157050

Other (OTH) AF: 0.767 AC: 11221 AN: 14626

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

African (AFR) AF: 0.720 AC: 29846 AN: 41476

American (AMR) AF: 0.751 AC: 11477 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3468

East Asian (EAS) AF: 0.889 AC: 4588 AN: 5158

South Asian (SAS) AF: 0.784 AC: 3776 AN: 4818

European-Finnish (FIN) AF: 0.782 AC: 8282 AN: 10596

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51134 AN: 67972

Other (OTH) AF: 0.768 AC: 1625 AN: 2116

Alfa AF: 0.756 Hom.: 174524

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
PhyloP100		2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs2848634; hg19: chr11-57252328;