5-151371996-A-G

Variant names:

• chr5-151371996-A-G
• rs13357969
• XM_011537591.2:c.-90+27262A>G

Variant summary

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

The ENST00000647906.1(ENSG00000290991):​n.1057-5338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,992 control chromosomes in the GnomAD database, including 22,700 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 0.52 (22700 hom., cov: 31)
• Consequence: ENSG00000290991 ENST00000647906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• 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]

ENSG00000253897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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.951-5338T>C		intron	N/A
	ENSG00000290991	ENST00000647906.1		n.1057-5338T>C		intron	N/A
	ENSG00000297368	ENST00000747508.1		n.675+27262A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78526 AN: 151874 Hom.: 22648 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.517 AC: 78636 AN: 151992 Hom.: 22700 Cov.: 31 AF XY: 0.516 AC XY: 38340 AN XY: 74268

African (AFR) AF: 0.791 AC: 32823 AN: 41470

American (AMR) AF: 0.356 AC: 5440 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1409 AN: 3464

East Asian (EAS) AF: 0.566 AC: 2931 AN: 5174

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4818

European-Finnish (FIN) AF: 0.493 AC: 5191 AN: 10538

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27166 AN: 67944

Other (OTH) AF: 0.478 AC: 1010 AN: 2112

Alfa AF: 0.465 Hom.: 14076

Bravo AF: 0.518

Asia WGS AF: 0.535 AC: 1857 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	3.4
DANN	Benign	0.78
PhyloP100		0.25

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: rs13357969;

hg19: chr5-150751557;