Genetic Variant SLC50A1:n.299G>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 ENST00000465546.5(SLC50A1):n.299G>A variant causes a splice region, non coding transcript exon 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
ENST00000465546.5 splice_region, non_coding_transcript_exon

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:

Genome browser will be placed here

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC50A1	NM_018845.4 link	c.-221G>A		upstream_gene_variant		ENST00000368404.9	NP_061333.2	Q9BRV3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC50A1	ENST00000368404.9 link	c.-221G>A		upstream_gene_variant		1	NM_018845.4	ENSP00000357389.4		Q9BRV3-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over