rs1497474

chr12-59680008-G-A

Variant summary

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

The NM_001270623.2(SLC16A7):c.-31+24758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,872 control chromosomes in the GnomAD database, including 8,578 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 0.32 (8578 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.-31+24758G>A		intron_variant		ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-31+24758G>A		intron_variant		1	NM_001270623.2	P1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49102 AN: 151754 Hom.: 8542 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.324 AC: 49196 AN: 151872 Hom.: 8578 Cov.: 32 AF XY: 0.325 AC XY: 24093 AN XY: 74214

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.310

Alfa AF: 0.290 Hom.: 4666

Bravo AF: 0.325

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.1
Dann	Benign	0.54

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: rs1497474; hg19: chr12-60073789;