rs714368

Variant names:

• chr6-110456925-T-A
• rs714368
• NM_033125.4:c.146A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-110456925-T-A
• chr6-110456925-T-C
• chr6-110456925-T-G

Variant summary

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

The NM_033125.4(SLC22A16):​c.146A>T​(p.His49Leu) 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SLC22A16 NM_033125.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• Publications: 0 publications found

Genes affected

SLC22A16 (HGNC:20302): (solute carrier family 22 member 16) This gene encodes a member of the organic zwitterion transporter protein family which transports carnitine. The encoded protein has also been shown to transport anticancer drugs like bleomycin (PMID: 20037140) successful treatment has been correlated with the level of activity of this transporter in tumor cells. [provided by RefSeq, Dec 2011]

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=0.15277746).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A16	NM_033125.4	c.146A>T	p.His49Leu	missense_variant	Exon 2 of 8	ENST00000368919.8	NP_149116.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A16	ENST00000368919.8	c.146A>T	p.His49Leu	missense_variant	Exon 2 of 8	1	NM_033125.4	ENSP00000357915.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.065	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	0.12
DANN	Benign	0.57
DEOGEN2	Benign	0.15	T;.;.;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.20	T;T;T;T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.15	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.55	N;.;.;.
PhyloP100		0.85
PrimateAI	Benign	0.20	T
PROVEAN	Uncertain	-2.6	D;D;N;N
REVEL	Benign	0.23
Sift	Uncertain	0.016	D;T;D;T
Sift4G	Benign	0.12	T;T;.;T
Polyphen		0.0	B;B;.;.
Vest4		0.14
MutPred		0.44		Loss of disorder (P = 0.0372);.;.;.;
MVP		0.048
MPC		0.016
ClinPred		0.054	T
GERP RS		-3.1
PromoterAI		-0.011	Neutral
Varity_R		0.11
gMVP		0.50
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs714368; hg19: chr6-110778128;