14-60984871-C-T

Variant names:

• chr14-60984871-C-T
• rs2149303
• NM_153811.3:c.310+68C>T

Variant summary

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

The NM_153811.3(SLC38A6):​c.310+68C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 1,405,510 control chromosomes in the GnomAD database, including 642,554 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 (66406 hom., cov: 32)
  • Exomes 𝑓: 0.96 (576148 hom.)
• Consequence: SLC38A6 NM_153811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 5 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=-0.95).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A6	NM_153811.3	MANE Select	c.310+68C>T		intron	N/A	NP_722518.2	Q8IZM9-1
	SLC38A6	NM_001172702.2		c.310+68C>T		intron	N/A	NP_001166173.1	Q8IZM9-2
	SLC38A6	NR_033344.2		n.652+68C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A6	ENST00000267488.9	TSL:1 MANE Select	c.310+68C>T		intron	N/A	ENSP00000267488.4	Q8IZM9-1
	SLC38A6	ENST00000354886.6	TSL:1	c.310+68C>T		intron	N/A	ENSP00000346959.2	Q8IZM9-2
	SLC38A6	ENST00000451406.5	TSL:1	c.295+68C>T		intron	N/A	ENSP00000395851.1	A0A0C4DG39

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141665 AN: 152104 Hom.: 66365 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.934

GnomAD4 exome AF: 0.956 AC: 1198259 AN: 1253288 Hom.: 576148 AF XY: 0.952 AC XY: 603292 AN XY: 633720

African (AFR) AF: 0.879 AC: 25558 AN: 29072

American (AMR) AF: 0.835 AC: 36579 AN: 43784

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 23458 AN: 24688

East Asian (EAS) AF: 0.721 AC: 27774 AN: 38510

South Asian (SAS) AF: 0.795 AC: 64525 AN: 81212

European-Finnish (FIN) AF: 0.991 AC: 49453 AN: 49906

Middle Eastern (MID) AF: 0.947 AC: 4360 AN: 4606

European-Non Finnish (NFE) AF: 0.987 AC: 916052 AN: 928354

Other (OTH) AF: 0.950 AC: 50500 AN: 53156

GnomAD4 genome AF: 0.931 AC: 141766 AN: 152222 Hom.: 66406 Cov.: 32 AF XY: 0.927 AC XY: 68974 AN XY: 74444

African (AFR) AF: 0.879 AC: 36482 AN: 41492

American (AMR) AF: 0.883 AC: 13503 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3967 AN: 5180

South Asian (SAS) AF: 0.778 AC: 3753 AN: 4822

European-Finnish (FIN) AF: 0.989 AC: 10506 AN: 10618

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

European-Non Finnish (NFE) AF: 0.986 AC: 67114 AN: 68034

Other (OTH) AF: 0.929 AC: 1963 AN: 2112

Alfa AF: 0.957 Hom.: 10193

Bravo AF: 0.923

Asia WGS AF: 0.769 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.51
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2149303; hg19: chr14-61451589;