rs10445407

Positions:

• chr17-81288009-C-A
• chr17-81288009-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037984.3(SLC38A10):​c.217+1682G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,152 control chromosomes in the GnomAD database, including 21,364 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 0.52 (21364 hom., cov: 33)
• Consequence: SLC38A10 NM_001037984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC38A10	NM_001037984.3	c.217+1682G>T		intron_variant		ENST00000374759.8	NP_001033073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759.8	c.217+1682G>T		intron_variant		5	NM_001037984.3	ENSP00000363891	A2
SLC38A10	ENST00000288439.9	c.217+1682G>T		intron_variant		1		ENSP00000288439	P2
SLC38A10	ENST00000539748.1	c.73+1682G>T		intron_variant		3		ENSP00000439115

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78544 AN: 152034 Hom.: 21335 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.495

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.517 AC: 78625 AN: 152152 Hom.: 21364 Cov.: 33 AF XY: 0.511 AC XY: 38003 AN XY: 74362

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.491

Alfa AF: 0.456 Hom.: 5151

Bravo AF: 0.528

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.35

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

Other links and lift over

dbSNP: rs10445407; hg19: chr17-79261809;