rs2271090

Positions:

• chr17-81272805-A-G

Variant summary

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

The NM_001037984.3(SLC38A10):​c.913-178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,044 control chromosomes in the GnomAD database, including 22,584 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 0.51 (22584 hom., cov: 32)
• Consequence: SLC38A10 NM_001037984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC38A10	NM_001037984.3	c.913-178T>C		intron_variant		ENST00000374759.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC38A10	ENST00000374759.8	c.913-178T>C		intron_variant		5	NM_001037984.3	A2
SLC38A10	ENST00000288439.9	c.913-178T>C		intron_variant		1		P2
SLC38A10	ENST00000542075.5	n.1515-178T>C		intron_variant, non_coding_transcript_variant		2
SLC38A10	ENST00000546352.1	n.440-1781T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77884 AN: 151926 Hom.: 22540 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.513 AC: 77983 AN: 152044 Hom.: 22584 Cov.: 32 AF XY: 0.504 AC XY: 37469 AN XY: 74316

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.481

Alfa AF: 0.440 Hom.: 15763

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs2271090; hg19: chr17-79246605;