11-63217396-T-A

Variant names:

• chr11-63217396-T-A
• rs11231409
• NM_199352.6:c.748A>T

Variant summary

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

The NM_199352.6(SLC22A25):​c.748A>T​(p.Ser250Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 14/22 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: 32)
• Consequence: SLC22A25 NM_199352.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 29 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.748A>T	p.Ser250Cys	missense	Exon 7 of 12	NP_955384.3	Q6T423
	SLC22A25	NM_001394058.1		c.748A>T	p.Ser250Cys	missense	Exon 7 of 10	NP_001380987.1
	SLC22A25	NM_001394059.1		c.748A>T	p.Ser250Cys	missense	Exon 7 of 10	NP_001380988.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A25	ENST00000306494.11	TSL:1 MANE Select	c.748A>T	p.Ser250Cys	missense	Exon 7 of 12	ENSP00000307443.6	Q6T423
	SLC22A25	ENST00000527057.5	TSL:1	n.742A>T		non_coding_transcript_exon	Exon 4 of 10	ENSP00000432242.1	H0YCS4
	SLC22A25	ENST00000528239.5	TSL:1	n.*397A>T		non_coding_transcript_exon	Exon 6 of 11	ENSP00000431235.1	H0YCA2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 50

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.094	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Uncertain	0.98
DEOGEN2	Benign	0.25	T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.86
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.47	T
M_CAP	Benign	0.0080	T
MetaRNN	Uncertain	0.58	D
MetaSVM	Benign	-0.76	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.32
PrimateAI	Benign	0.33	T
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.19
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0060	D
Polyphen		0.97	D
Vest4		0.25
MutPred		0.54		Loss of glycosylation at S250 (P = 0.0854)
MVP		0.26
MPC		0.067
ClinPred		0.86	D
GERP RS		0.35
Varity_R		0.32
gMVP		0.091
Mutation Taster		=100/0	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: rs11231409; hg19: chr11-62984868;