17-81261988-T-C

Variant names:

• chr17-81261988-T-C
• rs7224668
• NM_001037984.3:c.1132-1594A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037984.3(SLC38A10):​c.1132-1594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,166 control chromosomes in the GnomAD database, including 30,727 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 0.62 (30727 hom., cov: 34)
• Consequence: SLC38A10 NM_001037984.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 15 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC38A10	NM_001037984.3	c.1132-1594A>G		intron_variant	Intron 10 of 15	ENST00000374759.8	NP_001033073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC38A10	ENST00000374759.8	c.1132-1594A>G		intron_variant	Intron 10 of 15	5	NM_001037984.3	ENSP00000363891.3
SLC38A10	ENST00000288439.9	c.1132-1594A>G		intron_variant	Intron 10 of 13	1		ENSP00000288439.5
SLC38A10	ENST00000542075.5	n.1734-1594A>G		intron_variant	Intron 8 of 13	2
SLC38A10	ENST00000546352.1	n.547-1594A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93683 AN: 152048 Hom.: 30682 Cov.: 34

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.616 AC: 93781 AN: 152166 Hom.: 30727 Cov.: 34 AF XY: 0.608 AC XY: 45254 AN XY: 74386

African (AFR) AF: 0.852 AC: 35409 AN: 41544

American (AMR) AF: 0.546 AC: 8345 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1678 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5170

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5545 AN: 10576

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37433 AN: 67976

Other (OTH) AF: 0.591 AC: 1249 AN: 2114

Alfa AF: 0.568 Hom.: 36075

Bravo AF: 0.629

Asia WGS AF: 0.381 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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: rs7224668; hg19: chr17-79235788;