17-81290360-A-G

Variant names:

• chr17-81290360-A-G
• rs11150780
• NM_001037984.3:c.100-552T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 13 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001037984.3. 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
	SLC38A10	NM_001037984.3	MANE Select	c.100-552T>C		intron	N/A	NP_001033073.1
	SLC38A10	NM_138570.4		c.100-552T>C		intron	N/A	NP_612637.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A10	ENST00000374759.8	TSL:5 MANE Select	c.100-552T>C		intron	N/A	ENSP00000363891.3
	SLC38A10	ENST00000288439.9	TSL:1	c.100-552T>C		intron	N/A	ENSP00000288439.5
	SLC38A10	ENST00000539748.1	TSL:3	c.-45-552T>C		intron	N/A	ENSP00000439115.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46864 AN: 151962 Hom.: 7455 Cov.: 32

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

African (AFR) AF: 0.348 AC: 14440 AN: 41468

American (AMR) AF: 0.272 AC: 4158 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 505 AN: 3472

East Asian (EAS) AF: 0.133 AC: 690 AN: 5182

South Asian (SAS) AF: 0.165 AC: 794 AN: 4826

European-Finnish (FIN) AF: 0.311 AC: 3282 AN: 10562

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22008 AN: 67974

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.308 Hom.: 12549

Bravo AF: 0.307

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		0.14
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: rs11150780; hg19: chr17-79264160;