Genetic Variant SLC38A10:c.*642G>A (chr17-81244914-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001037984.3(SLC38A10):c.*642G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 163,124 control chromosomes in the GnomAD database, including 13,773 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 0.37 ( 12697 hom., cov: 33)

Exomes 𝑓: 0.43 ( 1076 hom. )

Consequence

SLC38A10
NM_001037984.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.81

Publications

16 publications found

Variant links:

Genes affected

SLC38A10 (HGNC:28237): (solute carrier family 38 member 10) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to act upstream of or within bone development. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

SLC38A10 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC38A10	NM_001037984.3 link	c.*642G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000374759.8	NP_001033073.1	Q9HBR0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759.8 link	c.*642G>A		3_prime_UTR_variant	Exon 16 of 16	5	NM_001037984.3	ENSP00000363891.3		Q9HBR0-1
SLC38A10	ENST00000539643.1 link	n.*90G>A		downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55706

AN:

152012

Hom.:

12695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0887

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.575

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.390

GnomAD4 exome

AF:

0.425

AC:

4675

AN:

10994

Hom.:

1076

AF XY:

0.429

AC XY:

2457

AN XY:

5728

show subpopulations

African (AFR)

AF:

0.0868

AC:

AN:

334

American (AMR)

AF:

0.415

AC:

113

AN:

272

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

149

AN:

300

East Asian (EAS)

AF:

0.650

AC:

655

AN:

1008

South Asian (SAS)

AF:

0.636

AC:

AN:

European-Finnish (FIN)

AF:

0.392

AC:

465

AN:

1186

Middle Eastern (MID)

AF:

0.667

AC:

AN:

European-Non Finnish (NFE)

AF:

0.412

AC:

2965

AN:

7194

Other (OTH)

AF:

0.377

AC:

215

AN:

570

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

121

243

364

486

607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.366

AC:

55715

AN:

152130

Hom.:

12697

Cov.:

AF XY:

0.374

AC XY:

27826

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0885

AC:

3677

AN:

41560

American (AMR)

AF:

0.454

AC:

6937

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.575

AC:

1994

AN:

3470

East Asian (EAS)

AF:

0.696

AC:

3600

AN:

5176

South Asian (SAS)

AF:

0.603

AC:

2909

AN:

4824

European-Finnish (FIN)

AF:

0.463

AC:

4887

AN:

10556

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30430

AN:

67946

Other (OTH)

AF:

0.392

AC:

829

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1602

3205

4807

6410

8012

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.440

Hom.:

18151

Bravo

AF:

0.353

Asia WGS

AF:

0.601

AC:

2088

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.41

(source)

DANN

Benign

0.62

PhyloP100

-2.8

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over