12-59680404-G-T

Variant names:

• chr12-59680404-G-T
• rs10877327
• NM_001270623.2:c.-30-24368G>T

Variant summary

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

The NM_001270623.2(SLC16A7):​c.-30-24368G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,186 control chromosomes in the GnomAD database, including 1,980 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 0.13 (1980 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.-30-24368G>T		intron_variant	Intron 2 of 5	ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-30-24368G>T		intron_variant	Intron 2 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19268 AN: 152068 Hom.: 1977 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.127 AC: 19272 AN: 152186 Hom.: 1980 Cov.: 32 AF XY: 0.130 AC XY: 9692 AN XY: 74428

African (AFR) AF: 0.0457 AC: 1898 AN: 41544

American (AMR) AF: 0.133 AC: 2038 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3466

East Asian (EAS) AF: 0.590 AC: 3038 AN: 5148

South Asian (SAS) AF: 0.196 AC: 949 AN: 4830

European-Finnish (FIN) AF: 0.109 AC: 1156 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9150 AN: 67994

Other (OTH) AF: 0.130 AC: 275 AN: 2116

Alfa AF: 0.124 Hom.: 1806

Bravo AF: 0.128

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.56
PhyloP100		0.51
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: rs10877327; hg19: chr12-60074185;