rs72552271

Variant names:

• chr1-112913980-C-G
• rs72552271
• NM_003051.4:c.1414G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-112913980-C-G
• chr1-112913980-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003051.4(SLC16A1):​c.1414G>C​(p.Gly472Arg) 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC16A1 NM_003051.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 0 publications found

Genes affected

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25446635).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.1414G>C	p.Gly472Arg	missense_variant	Exon 5 of 5	ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.1414G>C	p.Gly472Arg	missense_variant	Exon 5 of 5		NP_001159968.1
SLC16A1	XM_047428789.1	c.1414G>C	p.Gly472Arg	missense_variant	Exon 5 of 5		XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.1414G>C	p.Gly472Arg	missense_variant	Exon 5 of 5	1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.21
DEOGEN2	Benign	0.096	T;T
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.20	N
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.25	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-0.34	N;N
PhyloP100		1.6
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.070	N;N
REVEL	Benign	0.047
Sift	Benign	0.48	T;T
Sift4G	Benign	0.37	T;T
Polyphen		0.067	B;B
Vest4		0.44
MutPred		0.65		Gain of solvent accessibility (P = 0.0097);Gain of solvent accessibility (P = 0.0097);
MVP		0.21
MPC		0.40
ClinPred		0.35	T
GERP RS		4.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.12
gMVP		0.30
Mutation Taster		=92/8	polymorphism

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: rs72552271; hg19: chr1-113456602;