Genetic Variant SLC16A1-AS1:n.50G>C (chr1-112956453-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000416193.7(SLC16A1-AS1):n.50G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00656 in 335,064 control chromosomes in the GnomAD database, including 86 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 0.0035 ( 16 hom., cov: 31)

Exomes 𝑓: 0.0091 ( 70 hom. )

Consequence

SLC16A1-AS1
ENST00000416193.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

Publications

3 publications found

Variant links:

Genes affected

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

SLC16A1-AS1 links:

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

SLC16A1 Gene-Disease associations (from GenCC):

ketoacidosis due to monocarboxylate transporter-1 deficiency
Inheritance: AD, AR, SD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
exercise-induced hyperinsulinism
Inheritance: AD, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
disorder of fatty acid and ketone body metabolism
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
metabolic myopathy due to lactate transporter defect
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

SLC16A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1-AS1	NR_103743.1 link	n.39G>C		non_coding_transcript_exon_variant	Exon 1 of 3
SLC16A1-AS1	NR_103744.1 link	n.39G>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SLC16A1-AS1	ENST00000416193.7 link	n.50G>C	non_coding_transcript_exon_variant	Exon 1 of 3	1
SLC16A1-AS1	ENST00000428411.6 link	n.39G>C	non_coding_transcript_exon_variant	Exon 1 of 3	1
SLC16A1-AS1	ENST00000435800.7 link	n.44G>C	non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.00351

AC:

534

AN:

152022

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00688

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.0666

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.00336

GnomAD4 exome

AF:

0.00910

AC:

1665

AN:

182924

Hom.:

Cov.:

AF XY:

0.00867

AC XY:

808

AN XY:

93244

show subpopulations

African (AFR)

AF:

0.000758

AC:

AN:

5276

American (AMR)

AF:

0.00746

AC:

AN:

5226

Ashkenazi Jewish (ASJ)

AF:

0.00915

AC:

AN:

6886

East Asian (EAS)

AF:

0.0835

AC:

1448

AN:

17336

South Asian (SAS)

AF:

0.00122

AC:

AN:

1636

European-Finnish (FIN)

AF:

0.00

AC:

AN:

15066

Middle Eastern (MID)

AF:

0.00

AC:

AN:

990

European-Non Finnish (NFE)

AF:

0.000380

AC:

AN:

118368

Other (OTH)

AF:

0.00527

AC:

AN:

12140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

127

190

254

317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.00351

AC:

534

AN:

152140

Hom.:

Cov.:

AF XY:

0.00399

AC XY:

297

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.000193

AC:

AN:

41552

American (AMR)

AF:

0.00694

AC:

106

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00778

AC:

AN:

3470

East Asian (EAS)

AF:

0.0666

AC:

341

AN:

5122

South Asian (SAS)

AF:

0.00581

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000250

AC:

AN:

67972

Other (OTH)

AF:

0.00332

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

114

143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.000108

Hom.:

Bravo

AF:

0.00431

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.5

(source)

DANN

Benign

0.44

PhyloP100

-2.1

PromoterAI

-0.17

Neutral

(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