Genetic Variant SLC16A7:c.-30-8346G>C (chr12-59696426-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 NM_001270623.2(SLC16A7):c.-30-8346G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,634 control chromosomes in the GnomAD database, including 4,420 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 0.24 ( 4420 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

SLC16A7
NM_001270623.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0810

Publications

3 publications found

Variant links:

Genes affected

SLC16A7 (HGNC:10928): (solute carrier family 16 member 7) This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

SLC16A7 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001270623.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC16A7	NM_001270623.2	MANE Select	c.-30-8346G>C	intron	N/A	NP_001257552.1
SLC16A7	NM_001270622.2		c.-10-8366G>C	intron	N/A	NP_001257551.1
SLC16A7	NM_004731.5		c.-31+6956G>C	intron	N/A	NP_004722.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.-30-8346G>C	intron	N/A	ENSP00000448071.1
SLC16A7	ENST00000261187.8	TSL:1	c.-31+6956G>C	intron	N/A	ENSP00000261187.4
SLC16A7	ENST00000552432.5	TSL:1	c.-10-8366G>C	intron	N/A	ENSP00000449547.1

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36222

AN:

151516

Hom.:

4417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.223

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.239

AC:

36244

AN:

151634

Hom.:

4420

Cov.:

AF XY:

0.239

AC XY:

17726

AN XY:

74066

show subpopulations

African (AFR)

AF:

0.271

AC:

11225

AN:

41406

American (AMR)

AF:

0.221

AC:

3352

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

929

AN:

3462

East Asian (EAS)

AF:

0.126

AC:

645

AN:

5122

South Asian (SAS)

AF:

0.240

AC:

1158

AN:

4818

European-Finnish (FIN)

AF:

0.256

AC:

2699

AN:

10526

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15566

AN:

67794

Other (OTH)

AF:

0.220

AC:

463

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1420

2839

4259

5678

7098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.240

Hom.:

567

Bravo

AF:

0.234

Asia WGS

AF:

0.188

AC:

655

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.83

(source)

DANN

Benign

0.56

PhyloP100

0.081

Mutation Taster

=291/9

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over