Genetic Variant SLC50A1:c.-17+93G>A (chr1-155135691-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0900

Publications

23 publications found

Variant links:

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]

SLC50A1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BS2

High Homozygotes in GnomAd4 at 29 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287591.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC50A1	NM_001287591.2	c.-17+93G>A	intron	N/A	NP_001274520.1
SLC50A1	NM_001287590.2	c.9+11G>A	intron	N/A	NP_001274519.1	Q5SR67
SLC50A1	NM_001287592.2	c.12+93G>A	intron	N/A	NP_001274521.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC50A1	ENST00000484157.5	TSL:3	c.9+11G>A	intron	N/A	ENSP00000420189.1	Q5SR67
SLC50A1	ENST00000465546.5	TSL:3	n.299G>A	splice_region non_coding_transcript_exon	Exon 1 of 4
SLC50A1	ENST00000475824.6	TSL:5	n.9+11G>A	intron	N/A	ENSP00000497719.1	A0A3B3ITH1

Frequencies

GnomAD3 genomes

AF:

0.0112

AC:

1701

AN:

152238

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0114

AC:

1684

AN:

147082

AF XY:

0.0108

show subpopulations

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 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.:

AF XY:

0.0135

AC XY:

9282

AN XY:

689448

show subpopulations

African (AFR)

AF:

0.00215

AC:

AN:

31590

American (AMR)

AF:

0.00305

AC:

109

AN:

35704

Ashkenazi Jewish (ASJ)

AF:

0.00429

AC:

108

AN:

25182

East Asian (EAS)

AF:

0.0000560

AC:

AN:

35738

South Asian (SAS)

AF:

0.00211

AC:

167

AN:

79224

European-Finnish (FIN)

AF:

0.0471

AC:

2258

AN:

47974

Middle Eastern (MID)

AF:

0.000714

AC:

AN:

5600

European-Non Finnish (NFE)

AF:

0.0151

AC:

16251

AN:

1078940

Other (OTH)

AF:

0.0101

AC:

588

AN:

57980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1033

2066

3098

4131

5164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

642

1284

1926

2568

3210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0112

AC:

1700

AN:

152356

Hom.:

Cov.:

AF XY:

0.0124

AC XY:

923

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.00257

AC:

107

AN:

41586

American (AMR)

AF:

0.00248

AC:

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.00248

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.0524

AC:

557

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0141

AC:

961

AN:

68032

Other (OTH)

AF:

0.00851

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

165

248

330

413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0114

Hom.:

Bravo

AF:

0.00724

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.93

(source)

DANN

Benign

0.79

PhyloP100

-0.090

PromoterAI

0.018

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over