12-59696426-G-C

Position:

• chr12-59696426-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.-30-8346G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,634 control chromosomes in the GnomAD database, including 4,420 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 0.24 (4420 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.-30-8346G>C		intron_variant		ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-30-8346G>C		intron_variant		1	NM_001270623.2	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36222 AN: 151516 Hom.: 4417 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.223

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.239 AC: 36244 AN: 151634 Hom.: 4420 Cov.: 32 AF XY: 0.239 AC XY: 17726 AN XY: 74066

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.220

Alfa AF: 0.240 Hom.: 567

Bravo AF: 0.234

Asia WGS AF: 0.188 AC: 655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.83
DANN	Benign	0.56

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: rs7971953; hg19: chr12-60090207;