rs995343

chr12-59685594-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.-30-19178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,890 control chromosomes in the GnomAD database, including 25,321 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 0.57 (25321 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.-30-19178G>A		intron_variant		ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-30-19178G>A		intron_variant		1	NM_001270623.2	P1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85954 AN: 151770 Hom.: 25284 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.566 AC: 86042 AN: 151890 Hom.: 25321 Cov.: 32 AF XY: 0.564 AC XY: 41833 AN XY: 74210

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.536

Alfa AF: 0.523 Hom.: 11544

Bravo AF: 0.566

Asia WGS AF: 0.427 AC: 1483 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.53
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: rs995343; hg19: chr12-60079375;