rs7700790

Positions:

• chr5-151366778-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011537591.2(SLC36A1):​c.-90+22044G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 153,038 control chromosomes in the GnomAD database, including 4,236 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 (4236 hom., cov: 32)
  • Exomes 𝑓: 0.017 (0 hom.)
• Consequence: SLC36A1 XM_011537591.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A1	XM_011537591.2	c.-90+22044G>T		intron_variant			XP_011535893.1
LOC105378234	XR_007059004.1	n.1345-13972C>A		intron_variant
LOC105378234	XR_007059005.1	n.1127-120C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253897	ENST00000517788.1	n.951-120C>A		intron_variant		6
ENSG00000290991	ENST00000647906.1	n.1057-120C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21392 AN: 152078 Hom.: 4221 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0166 AC: 14 AN: 842 Hom.: 0 AF XY: 0.0207 AC XY: 10 AN XY: 482

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00980

Gnomad4 OTH exome AF: 0.0741

GnomAD4 genome AF: 0.141 AC: 21449 AN: 152196 Hom.: 4236 Cov.: 32 AF XY: 0.136 AC XY: 10157 AN XY: 74414

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.0611

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0196

Gnomad4 NFE AF: 0.0200

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0922 Hom.: 328

Bravo AF: 0.158

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7700790; hg19: chr5-150746339;