rs2241960

Variant names:

• chr12-46186835-A-G
• rs2241960
• NM_030674.4:c.*2135T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-46186835-A-G
• chr12-46186835-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030674.4(SLC38A1):​c.*2135T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,152 control chromosomes in the GnomAD database, including 4,488 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 0.22 (4488 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC38A1 NM_030674.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 19 publications found

Genes affected

SLC38A1 (HGNC:13447): (solute carrier family 38 member 1) Amino acid transporters play essential roles in the uptake of nutrients, production of energy, chemical metabolism, detoxification, and neurotransmitter cycling. SLC38A1 is an important transporter of glutamine, an intermediate in the detoxification of ammonia and the production of urea. Glutamine serves as a precursor for the synaptic transmitter, glutamate (Gu et al., 2001 [PubMed 11325958]).[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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC38A1	NM_030674.4	c.*2135T>C		3_prime_UTR_variant	Exon 17 of 17	ENST00000398637.10	NP_109599.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC38A1	ENST00000398637.10	c.*2135T>C		3_prime_UTR_variant	Exon 17 of 17	1	NM_030674.4	ENSP00000381634.4

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34050 AN: 152034 Hom.: 4488 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.236

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.224 AC: 34045 AN: 152152 Hom.: 4488 Cov.: 32 AF XY: 0.222 AC XY: 16524 AN XY: 74358

African (AFR) AF: 0.0853 AC: 3545 AN: 41558

American (AMR) AF: 0.309 AC: 4717 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1441 AN: 5168

South Asian (SAS) AF: 0.124 AC: 599 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3097 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18991 AN: 67984

Other (OTH) AF: 0.233 AC: 492 AN: 2112

Alfa AF: 0.263 Hom.: 8503

Bravo AF: 0.225

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.63
PhyloP100		-0.018
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: rs2241960; hg19: chr12-46580618;