NM_001037984.3:c.1892C>T

Variant names:

• chr17-81252248-G-A
• rs61740860
• NM_001037984.3:c.1892C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001037984.3(SLC38A10):​c.1892C>T​(p.Pro631Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000547 in 1,556,240 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0012 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00047 (1 hom.)
• Consequence: SLC38A10 NM_001037984.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.35
• Publications: 0 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: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0046235025).
• BP6: Variant 17-81252248-G-A is Benign according to our data. Variant chr17-81252248-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2379787.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A10	NM_001037984.3	MANE Select	c.1892C>T	p.Pro631Leu	missense	Exon 13 of 16	NP_001033073.1	Q9HBR0-1
	SLC38A10	NM_138570.4		c.1892C>T	p.Pro631Leu	missense	Exon 13 of 14	NP_612637.1	Q9HBR0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A10	ENST00000374759.8	TSL:5 MANE Select	c.1892C>T	p.Pro631Leu	missense	Exon 13 of 16	ENSP00000363891.3	Q9HBR0-1
	SLC38A10	ENST00000288439.9	TSL:1	c.1892C>T	p.Pro631Leu	missense	Exon 13 of 14	ENSP00000288439.5	Q9HBR0-2
	SLC38A10	ENST00000947966.1		c.1892C>T	p.Pro631Leu	missense	Exon 13 of 18	ENSP00000618025.1

Frequencies

GnomAD3 genomes AF: 0.00122 AC: 186 AN: 152208 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000850

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.000479

GnomAD2 exomes AF: 0.000803 AC: 164 AN: 204148 AF XY: 0.000714

Gnomad AFR exome AF: 0.00271

Gnomad AMR exome AF: 0.000462

Gnomad ASJ exome AF: 0.00603

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00143

Gnomad NFE exome AF: 0.000431

Gnomad OTH exome AF: 0.00165

GnomAD4 exome AF: 0.000474 AC: 665 AN: 1403914 Hom.: 1 Cov.: 31 AF XY: 0.000460 AC XY: 319 AN XY: 693638

African (AFR) AF: 0.00439 AC: 137 AN: 31240

American (AMR) AF: 0.000513 AC: 18 AN: 35116

Ashkenazi Jewish (ASJ) AF: 0.00670 AC: 152 AN: 22700

East Asian (EAS) AF: 0.00 AC: 0 AN: 39070

South Asian (SAS) AF: 0.0000253 AC: 2 AN: 79188

European-Finnish (FIN) AF: 0.00168 AC: 82 AN: 48730

Middle Eastern (MID) AF: 0.00237 AC: 13 AN: 5494

European-Non Finnish (NFE) AF: 0.000179 AC: 194 AN: 1084676

Other (OTH) AF: 0.00116 AC: 67 AN: 57700

GnomAD4 genome AF: 0.00122 AC: 186 AN: 152326 Hom.: 1 Cov.: 33 AF XY: 0.00117 AC XY: 87 AN XY: 74486

African (AFR) AF: 0.00277 AC: 115 AN: 41578

American (AMR) AF: 0.000849 AC: 13 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000382 AC: 26 AN: 68018

Other (OTH) AF: 0.000474 AC: 1 AN: 2110

Alfa AF: 0.0772 Hom.: 2353

Bravo AF: 0.00144

ESP6500AA AF: 0.00137 AC: 6

ESP6500EA AF: 0.000585 AC: 5

ExAC AF: 0.000851 AC: 103

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.056
BayesDel_addAF	Benign	-0.60	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.079
DANN	Benign	0.49
DEOGEN2	Benign	0.00092	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0072	N
LIST_S2	Benign	0.65	T
M_CAP	Benign	0.0030	T
MetaRNN	Benign	0.0046	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.35	N
PhyloP100		-1.4
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.16	N
REVEL	Benign	0.036
Sift	Benign	1.0	T
Sift4G	Benign	0.82	T
Polyphen		0.0020	B
Vest4		0.11
MVP		0.076
MPC		0.12
ClinPred		0.00074	T
GERP RS		-0.55
PromoterAI		0.0072	Neutral
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.3
Varity_R		0.027
gMVP		0.11
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs61740860; hg19: chr17-79226048;