17-81290360-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001037984.3(SLC38A10):​c.100-552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,080 control chromosomes in the GnomAD database, including 7,460 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 0.31 ( 7460 hom., cov: 32)

Consequence

SLC38A10
NM_001037984.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.142
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC38A10NM_001037984.3 linkuse as main transcriptc.100-552T>C intron_variant ENST00000374759.8 NP_001033073.1 Q9HBR0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC38A10ENST00000374759.8 linkuse as main transcriptc.100-552T>C intron_variant 5 NM_001037984.3 ENSP00000363891.3 Q9HBR0-1
SLC38A10ENST00000288439.9 linkuse as main transcriptc.100-552T>C intron_variant 1 ENSP00000288439.5 Q9HBR0-2
SLC38A10ENST00000539748.1 linkuse as main transcriptc.-45-552T>C intron_variant 3 ENSP00000439115.1 F5H3T4
SLC38A10ENST00000540233.1 linkuse as main transcriptn.93-552T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.308
AC:
46864
AN:
151962
Hom.:
7455
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.348
Gnomad AMI
AF:
0.431
Gnomad AMR
AF:
0.272
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.133
Gnomad SAS
AF:
0.166
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.324
Gnomad OTH
AF:
0.283
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.308
AC:
46892
AN:
152080
Hom.:
7460
Cov.:
32
AF XY:
0.303
AC XY:
22495
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.348
Gnomad4 AMR
AF:
0.272
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.133
Gnomad4 SAS
AF:
0.165
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.324
Gnomad4 OTH
AF:
0.279
Alfa
AF:
0.308
Hom.:
9853
Bravo
AF:
0.307
Asia WGS
AF:
0.147
AC:
512
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
3.1
DANN
Benign
0.55

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs11150780; hg19: chr17-79264160; API