12-59710259-C-T

Position:

• chr12-59710259-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.217+5241C>T		intron_variant		ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.217+5241C>T		intron_variant		1	NM_001270623.2	ENSP00000448071	P1

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

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.265

Alfa AF: 0.273 Hom.: 9803

Bravo AF: 0.248

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.72

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

LitVar

Other links and lift over

dbSNP: rs12231740; hg19: chr12-60104040;