rs2706301

Positions:

• chr12-59741621-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.218-29598G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,074 control chromosomes in the GnomAD database, including 28,232 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 0.60 (28232 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.218-29598G>C		intron_variant		ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.218-29598G>C		intron_variant		1	NM_001270623.2	P1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91324 AN: 151954 Hom.: 28193 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.601 AC: 91419 AN: 152074 Hom.: 28232 Cov.: 32 AF XY: 0.600 AC XY: 44595 AN XY: 74338

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.569

Alfa AF: 0.589 Hom.: 3343

Bravo AF: 0.598

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.55

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: rs2706301; hg19: chr12-60135402;