12-59762265-T-G

Variant names:

• chr12-59762265-T-G
• rs10877333
• NM_001270623.2:c.218-8954T>G

Variant summary

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

The NM_001270623.2(SLC16A7):​c.218-8954T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,118 control chromosomes in the GnomAD database, including 2,000 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 0.15 (2000 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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.218-8954T>G		intron	N/A	NP_001257552.1
	SLC16A7	NM_001270622.2		c.218-8954T>G		intron	N/A	NP_001257551.1
	SLC16A7	NM_004731.5		c.218-8954T>G		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.218-8954T>G		intron	N/A	ENSP00000448071.1
	SLC16A7	ENST00000261187.8	TSL:1	c.218-8954T>G		intron	N/A	ENSP00000261187.4
	SLC16A7	ENST00000552432.5	TSL:1	c.218-8954T>G		intron	N/A	ENSP00000449547.1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22720 AN: 152000 Hom.: 1999 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22723 AN: 152118 Hom.: 2000 Cov.: 32 AF XY: 0.150 AC XY: 11185 AN XY: 74366

African (AFR) AF: 0.0615 AC: 2553 AN: 41540

American (AMR) AF: 0.168 AC: 2564 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5172

South Asian (SAS) AF: 0.0988 AC: 476 AN: 4820

European-Finnish (FIN) AF: 0.243 AC: 2570 AN: 10586

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13066 AN: 67966

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.174 Hom.: 1420

Bravo AF: 0.142

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.82
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: rs10877333; hg19: chr12-60156046;