5-151348120-A-G

Variant names:

• chr5-151348120-A-G
• rs10515647
• XM_011537591.2:c.-90+3386A>G

Variant summary

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

The ENST00000747508.1(ENSG00000297368):​n.675+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: ENSG00000297368 ENST00000747508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 1 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]

ENSG00000297368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747508.1. 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
	ENSG00000297368	ENST00000747508.1		n.675+3386A>G		intron	N/A

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

African (AFR) AF: 0.0671 AC: 2785 AN: 41524

American (AMR) AF: 0.104 AC: 1593 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1962 AN: 5154

South Asian (SAS) AF: 0.318 AC: 1527 AN: 4804

European-Finnish (FIN) AF: 0.183 AC: 1931 AN: 10580

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10288 AN: 67980

Other (OTH) AF: 0.144 AC: 305 AN: 2116

Alfa AF: 0.131 Hom.: 264

Bravo AF: 0.129

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.55
PhyloP100		-0.27

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: rs10515647;

hg19: chr5-150727681;