rs12726330

chr1-155135691-G-Achr1-155135691-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001287591.2(SLC50A1):c.-17+93G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,550,288 control chromosomes in the GnomAD database, including 229 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 0.011 (29 hom., cov: 33)
  • Exomes 𝑓: 0.014 (200 hom.)
• Consequence: SLC50A1 NM_001287591.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

SLC50A1 (HGNC:30657): (solute carrier family 50 member 1) Enables glucoside transmembrane transporter activity. Predicted to be involved in carbohydrate transport. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS2: High Homozygotes in GnomAd at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC50A1	NM_001287590.2	c.9+11G>A		intron_variant
SLC50A1	NM_001287591.2	c.-17+93G>A		intron_variant
SLC50A1	NM_001287592.2	c.12+93G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC50A1	ENST00000484157.5	c.9+11G>A		intron_variant		3
SLC50A1	ENST00000465546.5	n.299G>A		splice_region_variant, non_coding_transcript_exon_variant	1/4	3
SLC50A1	ENST00000475824.6	c.9+11G>A		intron_variant, NMD_transcript_variant		5
SLC50A1	ENST00000490770.5	n.242+93G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1701 AN: 152238 Hom.: 29 Cov.: 33

Gnomad AFR AF: 0.00258

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00249

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.00860

GnomAD3 exomes AF: 0.0114 AC: 1684 AN: 147082 Hom.: 25 AF XY: 0.0108 AC XY: 852 AN XY: 79216

Gnomad AFR exome AF: 0.00288

Gnomad AMR exome AF: 0.00284

Gnomad ASJ exome AF: 0.00453

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00234

Gnomad FIN exome AF: 0.0464

Gnomad NFE exome AF: 0.0141

Gnomad OTH exome AF: 0.00892

GnomAD4 exome AF: 0.0140 AC: 19555 AN: 1397932 Hom.: 200 Cov.: 31 AF XY: 0.0135 AC XY: 9282 AN XY: 689448

Gnomad4 AFR exome AF: 0.00215

Gnomad4 AMR exome AF: 0.00305

Gnomad4 ASJ exome AF: 0.00429

Gnomad4 EAS exome AF: 0.0000560

Gnomad4 SAS exome AF: 0.00211

Gnomad4 FIN exome AF: 0.0471

Gnomad4 NFE exome AF: 0.0151

Gnomad4 OTH exome AF: 0.0101

GnomAD4 genome AF: 0.0112 AC: 1700 AN: 152356 Hom.: 29 Cov.: 33 AF XY: 0.0124 AC XY: 923 AN XY: 74500

Gnomad4 AFR AF: 0.00257

Gnomad4 AMR AF: 0.00248

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00248

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.0113 Hom.: 16

Bravo AF: 0.00724

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.93
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12726330; hg19: chr1-155108167;