12-59710259-C-T

Variant names:

• chr12-59710259-C-T
• rs12231740
• NM_001270623.2:c.217+5241C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.217+5241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,968 control chromosomes in the GnomAD database, including 5,110 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 0.25 (5110 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 6 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	NM_001270623.2	MANE Select	c.217+5241C>T		intron	N/A	NP_001257552.1	O60669
	SLC16A7	NM_001270622.2		c.217+5241C>T		intron	N/A	NP_001257551.1	O60669
	SLC16A7	NM_004731.5		c.217+5241C>T		intron	N/A	NP_004722.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.217+5241C>T		intron	N/A	ENSP00000448071.1	O60669
	SLC16A7	ENST00000261187.8	TSL:1	c.217+5241C>T		intron	N/A	ENSP00000261187.4	O60669
	SLC16A7	ENST00000552432.5	TSL:1	c.217+5241C>T		intron	N/A	ENSP00000449547.1	O60669

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38549 AN: 151850 Hom.: 5112 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.264

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.254 AC: 38548 AN: 151968 Hom.: 5110 Cov.: 32 AF XY: 0.254 AC XY: 18891 AN XY: 74262

African (AFR) AF: 0.185 AC: 7663 AN: 41452

American (AMR) AF: 0.223 AC: 3401 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1863 AN: 5170

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2892 AN: 10550

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19630 AN: 67942

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.272 Hom.: 22027

Bravo AF: 0.248

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12231740; hg19: chr12-60104040;