12-59762265-T-G

Position:

• chr12-59762265-T-G

Variant summary

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

The NM_001270623.2(SLC16A7):​c.218-8954T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,118 control chromosomes in the GnomAD database, including 2,000 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 0.15 (2000 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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]

SLC16A7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.218-8954T>G		intron_variant		ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.218-8954T>G		intron_variant		1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22720 AN: 152000 Hom.: 1999 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22723 AN: 152118 Hom.: 2000 Cov.: 32 AF XY: 0.150 AC XY: 11185 AN XY: 74366

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.131

Alfa AF: 0.174 Hom.: 1280

Bravo AF: 0.142

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.59

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: rs10877333; hg19: chr12-60156046;