chr12-59685049-G-A

Variant names:

• chr12-59685049-G-A
• rs7976956
• NM_001270623.2:c.-30-19723G>A

Variant summary

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

The NM_001270623.2(SLC16A7):​c.-30-19723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,058 control chromosomes in the GnomAD database, including 2,414 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 0.16 (2414 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.-30-19723G>A		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.-30-19723G>A		intron_variant	Intron 2 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24648 AN: 151938 Hom.: 2416 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.162 AC: 24654 AN: 152058 Hom.: 2414 Cov.: 32 AF XY: 0.161 AC XY: 11996 AN XY: 74318

African (AFR) AF: 0.0566 AC: 2350 AN: 41516

American (AMR) AF: 0.172 AC: 2630 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 682 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1714 AN: 5146

South Asian (SAS) AF: 0.180 AC: 868 AN: 4812

European-Finnish (FIN) AF: 0.161 AC: 1702 AN: 10574

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13958 AN: 67956

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.192 Hom.: 5947

Bravo AF: 0.163

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		0.036
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: rs7976956; hg19: chr12-60078830;