12-59643989-T-G

Variant names:

• chr12-59643989-T-G
• rs982322
• NM_001270623.2:c.-129-11163T>G

Variant summary

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

The NM_001270623.2(SLC16A7):​c.-129-11163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,048 control chromosomes in the GnomAD database, including 9,317 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 0.31 (9317 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.-129-11163T>G		intron_variant	Intron 1 of 5	ENST00000547379.6	NP_001257552.1
SLC16A7	NM_001270622.2	c.-109-11163T>G		intron_variant	Intron 1 of 5		NP_001257551.1
SLC16A7	XM_011538989.3	c.-129-11163T>G		intron_variant	Intron 1 of 6		XP_011537291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-129-11163T>G		intron_variant	Intron 1 of 5	1	NM_001270623.2	ENSP00000448071.1
SLC16A7	ENST00000552432.5	c.-109-11163T>G		intron_variant	Intron 1 of 5	1		ENSP00000449547.1
SLC16A7	ENST00000552024.5	c.-261-11163T>G		intron_variant	Intron 1 of 6	5		ENSP00000448742.1
SLC16A7	ENST00000549465.5	c.-129-11163T>G		intron_variant	Intron 1 of 3	3		ENSP00000447555.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46827 AN: 151932 Hom.: 9267 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.309 AC: 46931 AN: 152048 Hom.: 9317 Cov.: 32 AF XY: 0.307 AC XY: 22847 AN XY: 74324

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.292

Alfa AF: 0.215 Hom.: 5415

Bravo AF: 0.327

Asia WGS AF: 0.488 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.71

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: rs982322; hg19: chr12-60037770;