chr12-59723765-T-C

Variant names:

• chr12-59723765-T-C
• rs1619563
• NM_001270623.2:c.217+18747T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.217+18747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,030 control chromosomes in the GnomAD database, including 1,493 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 0.12 (1493 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.217+18747T>C		intron_variant	Intron 3 of 5	ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.217+18747T>C		intron_variant	Intron 3 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18624 AN: 151912 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.123 AC: 18638 AN: 152030 Hom.: 1493 Cov.: 32 AF XY: 0.121 AC XY: 9027 AN XY: 74332

African (AFR) AF: 0.221 AC: 9159 AN: 41486

American (AMR) AF: 0.0792 AC: 1208 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3466

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5170

South Asian (SAS) AF: 0.169 AC: 814 AN: 4826

European-Finnish (FIN) AF: 0.0526 AC: 559 AN: 10622

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0867 AC: 5890 AN: 67898

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.114 Hom.: 175

Bravo AF: 0.124

Asia WGS AF: 0.110 AC: 380 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		0.087
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1619563; hg19: chr12-60117546;