rs10515647

Positions:

• chr5-151348120-A-G

Variant summary

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

The XM_011537591.2(SLC36A1):​c.-90+3386A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,118 control chromosomes in the GnomAD database, including 1,946 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 0.14 (1946 hom., cov: 32)
• Consequence: SLC36A1 XM_011537591.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

SLC36A1 (HGNC:18761): (solute carrier family 36 member 1) This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A1	XM_011537591.2	c.-90+3386A>G		intron_variant			XP_011535893.1
		n.151348120A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21414 AN: 152000 Hom.: 1947 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.141 AC: 21424 AN: 152118 Hom.: 1946 Cov.: 32 AF XY: 0.146 AC XY: 10842 AN XY: 74350

Gnomad4 AFR AF: 0.0671

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.144

Alfa AF: 0.132 Hom.: 261

Bravo AF: 0.129

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515647; hg19: chr5-150727681;