rs9285645

Variant names:

• chr5-151383977-C-T
• rs9285645
• XM_011537591.2:c.-89-27304C>T

Variant summary

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

The ENST00000647906.1(ENSG00000290991):​n.1057-17319G>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: ENSG00000290991 ENST00000647906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 0 publications found

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]

ENSG00000253897 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647906.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253897	ENST00000517788.1	TSL:6	n.950+3086G>A		intron	N/A
	ENSG00000290991	ENST00000647906.1		n.1057-17319G>A		intron	N/A
	ENSG00000297368	ENST00000747508.1		n.676-27304C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9285645;

hg19: chr5-150763538;

COSMIC: COSV72957606;