14-61020330-T-G

Variant names:

• chr14-61020330-T-G
• rs7148163
• NM_153811.3:c.403+750T>G

Variant summary

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

The NM_153811.3(SLC38A6):​c.403+750T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,166 control chromosomes in the GnomAD database, including 66,434 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 0.93 (66434 hom., cov: 32)
• Consequence: SLC38A6 NM_153811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740
• Publications: 0 publications found

Genes affected

SLC38A6 (HGNC:19863): (solute carrier family 38 member 6) Predicted to enable L-glutamine transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport and glutamine transport. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153811.3. 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
	SLC38A6	NM_153811.3	MANE Select	c.403+750T>G		intron	N/A	NP_722518.2
	SLC38A6	NM_001172702.2		c.403+750T>G		intron	N/A	NP_001166173.1
	SLC38A6	NR_033344.2		n.745+750T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A6	ENST00000267488.9	TSL:1 MANE Select	c.403+750T>G		intron	N/A	ENSP00000267488.4
	SLC38A6	ENST00000354886.6	TSL:1	c.403+750T>G		intron	N/A	ENSP00000346959.2
	SLC38A6	ENST00000451406.5	TSL:1	c.388+750T>G		intron	N/A	ENSP00000395851.1

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141674 AN: 152048 Hom.: 66391 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.932 AC: 141777 AN: 152166 Hom.: 66434 Cov.: 32 AF XY: 0.927 AC XY: 68957 AN XY: 74390

African (AFR) AF: 0.880 AC: 36527 AN: 41526

American (AMR) AF: 0.884 AC: 13518 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3286 AN: 3466

East Asian (EAS) AF: 0.771 AC: 3983 AN: 5166

South Asian (SAS) AF: 0.778 AC: 3750 AN: 4820

European-Finnish (FIN) AF: 0.989 AC: 10496 AN: 10608

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67063 AN: 67966

Other (OTH) AF: 0.930 AC: 1966 AN: 2114

Alfa AF: 0.958 Hom.: 9048

Bravo AF: 0.924

Asia WGS AF: 0.771 AC: 2675 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		0.74
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: rs7148163; hg19: chr14-61487048;