Genetic Variant SLC38A8:c.*9T>C (chr16-84009775-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080442.3(SLC38A8):c.*9T>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 0.177 in 1,611,486 control chromosomes in the GnomAD database, including 30,830 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 7292 hom., cov: 32)

Exomes 𝑓: 0.17 ( 23538 hom. )

Consequence

SLC38A8
NM_001080442.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.248

Variant links:

Genes affected

SLC38A8 (HGNC:32434): (solute carrier family 38 member 8) This gene encodes a putative sodium-dependent amino-acid/proton antiporter. The protein has eleven transmembrane domains, an extracellular N-terminus and an intracellular C-terminal tail. The protein is a member of the SLC38 sodium-coupled neutral amino acid transporter family of proteins. Mutations in this gene result in foveal hypoplasia with or without optic nerve misrouting and/or anterior segment dysgenesis. [provided by RefSeq, May 2014]

SLC38A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 16-84009775-A-G is Benign according to our data. Variant chr16-84009775-A-G is described in ClinVar as [Benign]. Clinvar id is 1261175.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC38A8	NM_001080442.3 link	c.*9T>C		3_prime_UTR_variant	Exon 11 of 11	ENST00000299709.8	NP_001073911.1	A6NNN8
SLC38A8	XM_017022946.1 link	c.*9T>C		3_prime_UTR_variant	Exon 12 of 12		XP_016878435.1	A6NNN8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC38A8	ENST00000299709 link	c.*9T>C		3_prime_UTR_variant	Exon 11 of 11	5	NM_001080442.3	ENSP00000299709.3		A6NNN8
SLC38A8	ENST00000568003.1 link	n.393T>C		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40107

AN:

151988

Hom.:

7280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.521

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.188

AC:

46773

AN:

249004

Hom.:

5612

AF XY:

0.178

AC XY:

24048

AN XY:

134736

show subpopulations

Gnomad AFR exome

AF:

0.531

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.140

Gnomad SAS exome

AF:

0.136

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.168

AC:

245026

AN:

1459380

Hom.:

23538

Cov.:

AF XY:

0.166

AC XY:

120427

AN XY:

725944

show subpopulations

Gnomad4 AFR exome

AF:

0.533

Gnomad4 AMR exome

AF:

0.206

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.264

AC:

40154

AN:

152106

Hom.:

7292

Cov.:

AF XY:

0.262

AC XY:

19460

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.521

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.150

Gnomad4 SAS

AF:

0.147

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.212

Hom.:

2922

Bravo

AF:

0.283

Asia WGS

AF:

0.190

AC:

663

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 08, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.89

DANN

Benign

0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over