12-59689707-C-T

Variant names:

• chr12-59689707-C-T
• rs1000708
• NM_001270623.2:c.-30-15065C>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.-30-15065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,714 control chromosomes in the GnomAD database, including 25,888 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 0.57 (25888 hom., cov: 31)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.-30-15065C>T		intron_variant	Intron 2 of 5	ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-30-15065C>T		intron_variant	Intron 2 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87123 AN: 151596 Hom.: 25849 Cov.: 31

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.575 AC: 87213 AN: 151714 Hom.: 25888 Cov.: 31 AF XY: 0.574 AC XY: 42500 AN XY: 74104

African (AFR) AF: 0.739 AC: 30614 AN: 41430

American (AMR) AF: 0.477 AC: 7257 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1732 AN: 3458

East Asian (EAS) AF: 0.474 AC: 2440 AN: 5150

South Asian (SAS) AF: 0.524 AC: 2517 AN: 4804

European-Finnish (FIN) AF: 0.529 AC: 5560 AN: 10512

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35274 AN: 67822

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.530 Hom.: 10986

Bravo AF: 0.574

Asia WGS AF: 0.472 AC: 1641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.47
PromoterAI		-0.024	Neutral
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: rs1000708; hg19: chr12-60083488;