chr5-151371996-A-G

Variant names:

• chr5-151371996-A-G
• rs13357969
• XM_011537591.2:c.-90+27262A>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+27262A>G 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: SLC36A1 XM_011537591.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC36A1	XM_011537591.2	c.-90+27262A>G		intron_variant	Intron 1 of 11		XP_011535893.1
LOC105378234	XR_007059004.1	n.1345-19190T>C		intron_variant	Intron 6 of 6
LOC105378234	XR_007059005.1	n.1127-5338T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253897	ENST00000517788.1	n.951-5338T>C		intron_variant	Intron 8 of 8	6
ENSG00000290991	ENST00000647906.1	n.1057-5338T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.478

Alfa AF: 0.397 Hom.: 5824

Bravo AF: 0.518

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13357969; hg19: chr5-150751557;