17-81244914-C-T

Variant names:

• chr17-81244914-C-T
• rs2659005
• NM_001037984.3:c.*642G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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 (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC38A10	NM_001037984.3	c.*642G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000374759.8	NP_001033073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759.8	c.*642G>A		3_prime_UTR_variant	Exon 16 of 16	5	NM_001037984.3	ENSP00000363891.3
SLC38A10	ENST00000539643.1	n.*90G>A		downstream_gene_variant		1

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

African (AFR) AF: 0.0868 AC: 29 AN: 334

American (AMR) AF: 0.415 AC: 113 AN: 272

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 149 AN: 300

East Asian (EAS) AF: 0.650 AC: 655 AN: 1008

South Asian (SAS) AF: 0.636 AC: 56 AN: 88

European-Finnish (FIN) AF: 0.392 AC: 465 AN: 1186

Middle Eastern (MID) AF: 0.667 AC: 28 AN: 42

European-Non Finnish (NFE) AF: 0.412 AC: 2965 AN: 7194

Other (OTH) AF: 0.377 AC: 215 AN: 570

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

African (AFR) AF: 0.0885 AC: 3677 AN: 41560

American (AMR) AF: 0.454 AC: 6937 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3600 AN: 5176

South Asian (SAS) AF: 0.603 AC: 2909 AN: 4824

European-Finnish (FIN) AF: 0.463 AC: 4887 AN: 10556

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30430 AN: 67946

Other (OTH) AF: 0.392 AC: 829 AN: 2114

Alfa AF: 0.440 Hom.: 18151

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2659005; hg19: chr17-79218714;