rs12718000

Positions:

• chr12-59775484-G-A
• chr12-59775484-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.1180+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0938 in 1,599,018 control chromosomes in the GnomAD database, including 8,680 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 0.12 (1433 hom., cov: 32)
  • Exomes 𝑓: 0.091 (7247 hom.)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.1180+9G>A		intron_variant		ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.1180+9G>A		intron_variant		1	NM_001270623.2	ENSP00000448071	P1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18586 AN: 151980 Hom.: 1428 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.118

GnomAD3 exomes AF: 0.101 AC: 24783 AN: 244944 Hom.: 1755 AF XY: 0.106 AC XY: 14058 AN XY: 132532

Gnomad AFR exome AF: 0.214

Gnomad AMR exome AF: 0.0563

Gnomad ASJ exome AF: 0.161

Gnomad EAS exome AF: 0.0225

Gnomad SAS exome AF: 0.199

Gnomad FIN exome AF: 0.0542

Gnomad NFE exome AF: 0.0887

Gnomad OTH exome AF: 0.0997

GnomAD4 exome AF: 0.0908 AC: 131327 AN: 1446920 Hom.: 7247 Cov.: 28 AF XY: 0.0941 AC XY: 67764 AN XY: 720040

Gnomad4 AFR exome AF: 0.215

Gnomad4 AMR exome AF: 0.0594

Gnomad4 ASJ exome AF: 0.152

Gnomad4 EAS exome AF: 0.0397

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.0581

Gnomad4 NFE exome AF: 0.0811

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.122 AC: 18613 AN: 152098 Hom.: 1433 Cov.: 32 AF XY: 0.121 AC XY: 9003 AN XY: 74354

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0529

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0943 Hom.: 327

Bravo AF: 0.123

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.60

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: rs12718000; hg19: chr12-60169265; COSMIC: COSV53896379; COSMIC: COSV53896379;