NM_030674.4:c.903-256C>T

Variant names:

• chr12-46201454-G-A
• rs11183394
• NM_030674.4:c.903-256C>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.903-256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,058 control chromosomes in the GnomAD database, including 3,320 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 0.19 (3320 hom., cov: 31)
• Consequence: SLC38A1 NM_030674.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 2 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=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030674.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A1	NM_030674.4	MANE Select	c.903-256C>T		intron	N/A	NP_109599.3
	SLC38A1	NM_001278390.1		c.903-256C>T		intron	N/A	NP_001265319.1
	SLC38A1	NM_001077484.2		c.903-256C>T		intron	N/A	NP_001070952.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A1	ENST00000398637.10	TSL:1 MANE Select	c.903-256C>T		intron	N/A	ENSP00000381634.4
	SLC38A1	ENST00000552197.5	TSL:1	c.903-256C>T		intron	N/A	ENSP00000449756.1
	SLC38A1	ENST00000439706.5	TSL:1	c.903-256C>T		intron	N/A	ENSP00000398142.1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28409 AN: 151940 Hom.: 3318 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28434 AN: 152058 Hom.: 3320 Cov.: 31 AF XY: 0.183 AC XY: 13622 AN XY: 74336

African (AFR) AF: 0.335 AC: 13867 AN: 41442

American (AMR) AF: 0.134 AC: 2043 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3468

East Asian (EAS) AF: 0.0750 AC: 388 AN: 5174

South Asian (SAS) AF: 0.150 AC: 722 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1155 AN: 10564

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9279 AN: 67984

Other (OTH) AF: 0.184 AC: 390 AN: 2114

Alfa AF: 0.154 Hom.: 1355

Bravo AF: 0.193

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.8
DANN	Benign	0.90
PhyloP100		-0.60
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: rs11183394; hg19: chr12-46595237;