17-81244914-C-T

Position:

• chr17-81244914-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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

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=-0.9).
• 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/exons	MANE	Protein	UniProt
SLC38A10	NM_001037984.3	c.*642G>A		3_prime_UTR_variant	16/16	ENST00000374759.8	NP_001033073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759	c.*642G>A		3_prime_UTR_variant	16/16	5	NM_001037984.3	ENSP00000363891.3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55706 AN: 152012 Hom.: 12695 Cov.: 33

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

Gnomad4 AFR exome AF: 0.0868

Gnomad4 AMR exome AF: 0.415

Gnomad4 ASJ exome AF: 0.497

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.636

Gnomad4 FIN exome AF: 0.392

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.377

GnomAD4 genome AF: 0.366 AC: 55715 AN: 152130 Hom.: 12697 Cov.: 33 AF XY: 0.374 AC XY: 27826 AN XY: 74362

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.392

Alfa AF: 0.439 Hom.: 13853

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
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2659005; hg19: chr17-79218714;