17-7042338-C-G

Variant names:

• chr17-7042338-C-G
• NM_001370549.1:c.772G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001370549.1(SLC16A11):​c.772G>C​(p.Val258Leu) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC16A11 NM_001370549.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.382

Genes affected

SLC16A11 (HGNC:23093): (solute carrier family 16 member 11) Enables pyruvate transmembrane transporter activity. Involved in lipid metabolic process. Located in endoplasmic reticulum membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09862754).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A11	NM_001370549.1	c.772G>C	p.Val258Leu	missense_variant	Exon 4 of 5	ENST00000574600.3	NP_001357478.1
SLC16A11	NM_153357.3	c.772G>C	p.Val258Leu	missense_variant	Exon 3 of 4		NP_699188.2
SLC16A11	NM_001370553.1	c.772G>C	p.Val258Leu	missense_variant	Exon 4 of 4		NP_001357482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A11	ENST00000574600.3	c.772G>C	p.Val258Leu	missense_variant	Exon 4 of 5	3	NM_001370549.1	ENSP00000460927.2
SLC16A11	ENST00000573338.1	n.678-430G>C		intron_variant	Intron 1 of 1	1
SLC16A11	ENST00000662352.3	c.772G>C	p.Val258Leu	missense_variant	Exon 3 of 4			ENSP00000499634.1
SLC16A11	ENST00000673828.2	c.772G>C	p.Val258Leu	missense_variant	Exon 4 of 4			ENSP00000501313.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 18, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.844G>C (p.V282L) alteration is located in exon 3 (coding exon 3) of the SLC16A11 gene. This alteration results from a G to C substitution at nucleotide position 844, causing the valine (V) at amino acid position 282 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.84
DEOGEN2	Benign	0.042	T;.
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.65	D
LIST_S2	Benign	0.57	T;T
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.099	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-0.49	N;.
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	1.5	N;N
REVEL	Benign	0.063
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0080	B;.
Vest4		0.22
MutPred		0.71		Loss of catalytic residue at V282 (P = 0.0577);.;
MVP		0.28
MPC		0.40
ClinPred		0.087	T
GERP RS		3.1
Varity_R		0.12
gMVP		0.26

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-6945657;