12-59775484-G-A

Variant names:

• chr12-59775484-G-A
• rs12718000
• NM_001270623.2:c.1180+9G>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.1180+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0938 in 1,599,018 control chromosomes in the GnomAD database, including 8,680 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 (1433 hom., cov: 32)
  • Exomes 𝑓: 0.091 (7247 hom.)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001270623.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	NM_001270623.2	MANE Select	c.1180+9G>A		intron	N/A	NP_001257552.1
	SLC16A7	NM_001270622.2		c.1180+9G>A		intron	N/A	NP_001257551.1
	SLC16A7	NM_004731.5		c.1180+9G>A		intron	N/A	NP_004722.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.1180+9G>A		intron	N/A	ENSP00000448071.1
	SLC16A7	ENST00000261187.8	TSL:1	c.1180+9G>A		intron	N/A	ENSP00000261187.4
	SLC16A7	ENST00000552432.5	TSL:1	c.1180+9G>A		intron	N/A	ENSP00000449547.1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18586 AN: 151980 Hom.: 1428 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.118

GnomAD2 exomes AF: 0.101 AC: 24783 AN: 244944 AF XY: 0.106

Gnomad AFR exome AF: 0.214

Gnomad AMR exome AF: 0.0563

Gnomad ASJ exome AF: 0.161

Gnomad EAS exome AF: 0.0225

Gnomad FIN exome AF: 0.0542

Gnomad NFE exome AF: 0.0887

Gnomad OTH exome AF: 0.0997

GnomAD4 exome AF: 0.0908 AC: 131327 AN: 1446920 Hom.: 7247 Cov.: 28 AF XY: 0.0941 AC XY: 67764 AN XY: 720040

African (AFR) AF: 0.215 AC: 7103 AN: 32966

American (AMR) AF: 0.0594 AC: 2614 AN: 43974

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 3935 AN: 25818

East Asian (EAS) AF: 0.0397 AC: 1571 AN: 39596

South Asian (SAS) AF: 0.191 AC: 16287 AN: 85482

European-Finnish (FIN) AF: 0.0581 AC: 3091 AN: 53206

Middle Eastern (MID) AF: 0.188 AC: 1071 AN: 5690

European-Non Finnish (NFE) AF: 0.0811 AC: 89284 AN: 1100378

Other (OTH) AF: 0.107 AC: 6371 AN: 59810

GnomAD4 genome AF: 0.122 AC: 18613 AN: 152098 Hom.: 1433 Cov.: 32 AF XY: 0.121 AC XY: 9003 AN XY: 74354

African (AFR) AF: 0.212 AC: 8779 AN: 41486

American (AMR) AF: 0.0848 AC: 1295 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 550 AN: 3472

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5178

South Asian (SAS) AF: 0.189 AC: 912 AN: 4824

European-Finnish (FIN) AF: 0.0529 AC: 560 AN: 10578

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0884 AC: 6009 AN: 67972

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.0966 Hom.: 349

Bravo AF: 0.123

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		-0.53
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: rs12718000; hg19: chr12-60169265; COSMIC: COSV53896379; COSMIC: COSV53896379;