rs765385127

Variant names:

• chr22-38080879-C-A
• NM_013356.3:c.1159G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-38080879-C-A
• chr22-38080879-C-G
• chr22-38080879-C-T

Variant summary

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

The NM_013356.3(SLC16A8):​c.1159G>T​(p.Val387Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,397,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: SLC16A8 NM_013356.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

SLC16A8 (HGNC:16270): (solute carrier family 16 member 8) SLC16A8 is a member of a family of proton-coupled monocarboxylate transporters that mediate lactate transport across cell membranes (Yoon et al., 1999 [PubMed 10493836]).[supplied by OMIM, Apr 2010]

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=0.07106793).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A8	NM_013356.3	c.1159G>T	p.Val387Leu	missense_variant	Exon 5 of 6	ENST00000681075.2	NP_037488.2
SLC16A8	XM_017028685.2	c.1159G>T	p.Val387Leu	missense_variant	Exon 3 of 4		XP_016884174.1
SLC16A8	NM_001394131.1	c.-80-2175G>T		intron_variant	Intron 1 of 1		NP_001381060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A8	ENST00000681075.2	c.1159G>T	p.Val387Leu	missense_variant	Exon 5 of 6		NM_013356.3	ENSP00000506669.1
SLC16A8	ENST00000320521.10	c.1159G>T	p.Val387Leu	missense_variant	Exon 4 of 5	1		ENSP00000321735.5
SLC16A8	ENST00000469516.5	n.107-2175G>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.16e-7 AC: 1 AN: 1397566 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 691166

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000285

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.1
DANN	Benign	0.91
DEOGEN2	Benign	0.060	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.57	T
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.071	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.41	N
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.21
Sift	Benign	0.38	T
Sift4G	Benign	0.44	T
Polyphen		0.0060	B
Vest4		0.083
MutPred		0.62		Loss of catalytic residue at V387 (P = 0.1358);
MVP		0.19
MPC		0.21
ClinPred		0.042	T
GERP RS		-6.2
Varity_R		0.077
gMVP		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: chr22-38476886;