rs1238485866

Variant names:

• chr11-63164029-C-A
• rs1238485866
• NM_199352.6:c.1439G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-63164029-C-A
• chr11-63164029-C-T

Variant summary

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

The NM_199352.6(SLC22A25):​c.1439G>T​(p.Gly480Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. G480E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC22A25 NM_199352.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 4 publications found

Genes affected

SLC22A25 (HGNC:32935): (solute carrier family 22 member 25) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199352.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A25	NM_199352.6	MANE Select	c.1439G>T	p.Gly480Val	missense	Exon 12 of 12	NP_955384.3	Q6T423

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A25	ENST00000306494.11	TSL:1 MANE Select	c.1439G>T	p.Gly480Val	missense	Exon 12 of 12	ENSP00000307443.6	Q6T423
	SLC22A25	ENST00000525295.1	TSL:1	n.*692G>T		non_coding_transcript_exon	Exon 7 of 7	ENSP00000435614.1	E9PJ86
	SLC22A25	ENST00000527057.5	TSL:1	n.*388G>T		non_coding_transcript_exon	Exon 10 of 10	ENSP00000432242.1	H0YCS4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	3.9
DANN	Benign	0.77
DEOGEN2	Benign	0.15	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.021	N
LIST_S2	Benign	0.64	T
M_CAP	Benign	0.0070	T
MetaRNN	Uncertain	0.57	D
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	2.0	M
PhyloP100		0.0080
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.17
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.014	D
Polyphen		0.37	B
Vest4		0.35
MutPred		0.81		Loss of catalytic residue at I478 (P = 0.1797)
MVP		0.21
MPC		0.033
ClinPred		0.32	T
GERP RS		-2.2
Varity_R		0.12
gMVP		0.54
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs1238485866; hg19: chr11-62931501;