rs9285645

Variant names:

• chr5-151383977-C-T
• rs9285645
• ENST00000517788.1:n.950+3086G>A

Variant summary

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

The ENST00000517788.1(ENSG00000253897):​n.950+3086G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,748 control chromosomes in the GnomAD database, including 7,911 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 0.29 (7911 hom., cov: 31)
• Consequence: ENSG00000253897 ENST00000517788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 0 publications found

Genes affected

ENSG00000253897 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC36A1	XM_011537591.2	c.-89-27304C>T		intron_variant	Intron 1 of 11		XP_011535893.1
LOC105378234	XR_007059004.1	n.1344+28555G>A		intron_variant	Intron 6 of 6
LOC105378234	XR_007059005.1	n.1127-17319G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253897	ENST00000517788.1	n.950+3086G>A		intron_variant	Intron 8 of 8	6
ENSG00000290991	ENST00000647906.1	n.1057-17319G>A		intron_variant	Intron 3 of 3
ENSG00000297368	ENST00000747508.1	n.676-27304C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44558 AN: 151630 Hom.: 7897 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.294 AC: 44610 AN: 151748 Hom.: 7911 Cov.: 31 AF XY: 0.289 AC XY: 21406 AN XY: 74094

African (AFR) AF: 0.492 AC: 20350 AN: 41338

American (AMR) AF: 0.195 AC: 2971 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3464

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5174

South Asian (SAS) AF: 0.137 AC: 661 AN: 4812

European-Finnish (FIN) AF: 0.283 AC: 2955 AN: 10448

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16265 AN: 67920

Other (OTH) AF: 0.262 AC: 554 AN: 2114

Alfa AF: 0.296 Hom.: 961

Bravo AF: 0.295

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.76
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs9285645; hg19: chr5-150763538; COSMIC: COSV72957606;