Genetic Variant NM_001270623.2:c.331C>G (chr12-59771332-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_001270623.2(SLC16A7):c.331C>G(p.Gln111Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)

Consequence

SLC16A7
NM_001270623.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.118

Publications

0 publications found

Variant links:

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]

SLC16A7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.07659808).

BP6

Variant 12-59771332-C-G is Benign according to our data. Variant chr12-59771332-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2289418.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC16A7	NM_001270623.2	MANE Select	c.331C>G	p.Gln111Glu	missense	Exon 4 of 6	NP_001257552.1	O60669
SLC16A7	NM_001270622.2		c.331C>G	p.Gln111Glu	missense	Exon 4 of 6	NP_001257551.1	O60669
SLC16A7	NM_004731.5		c.331C>G	p.Gln111Glu	missense	Exon 3 of 5	NP_004722.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.331C>G	p.Gln111Glu	missense	Exon 4 of 6	ENSP00000448071.1	O60669
SLC16A7	ENST00000261187.8	TSL:1	c.331C>G	p.Gln111Glu	missense	Exon 3 of 5	ENSP00000261187.4	O60669
SLC16A7	ENST00000552432.5	TSL:1	c.331C>G	p.Gln111Glu	missense	Exon 4 of 6	ENSP00000449547.1	O60669

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.049

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.043

(source)

DANN

Benign

0.075

DEOGEN2

Benign

0.13

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.55

M_CAP

Uncertain

0.087

MetaRNN

Benign

0.077

MetaSVM

Benign

-0.70

MutationAssessor

Benign

-0.38

PhyloP100

-0.12

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.080

REVEL

Benign

0.11

Sift

Benign

0.95

Sift4G

Benign

0.99

Polyphen

0.0010

Vest4

0.29

MutPred

0.51

Gain of catalytic residue at S107 (P = 0)

MVP

0.34

MPC

0.066

ClinPred

0.016

GERP RS

-11

Varity_R

0.15

gMVP

0.61

Mutation Taster

=94/6

polymorphism

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over