Variant 11-63143607-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001136506.2(SLC22A24):c.173C>G(p.Thr58Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 1,574,552 control chromosomes in the GnomAD database, including 551,601 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 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: 𝑓 0.76 ( 45537 hom., cov: 31)

Exomes 𝑓: 0.84 ( 506064 hom. )

Consequence

SLC22A24
NM_001136506.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.110

Variant links:

Genes affected

SLC22A24 (HGNC:28542): (solute carrier family 22 member 24) SLC22A24 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]

SLC22A24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.0526675E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A24	NM_001136506.2 link	c.173C>G	p.Thr58Ser	missense_variant	1/10	ENST00000612278.4	NP_001129978.2	Q8N4F4-2
SLC22A24	NM_173586.3 link	c.173C>G	p.Thr58Ser	missense_variant	1/4		NP_775857.2	Q8N4F4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC22A24	ENST00000612278.4 link	c.173C>G	p.Thr58Ser	missense_variant	1/10	5	NM_001136506.2	ENSP00000480336.1	Q8N4F4-2
SLC22A24	ENST00000417740.5 link	c.173C>G	p.Thr58Ser	missense_variant	1/10	5		ENSP00000396586.1	Q8N4F4-3
SLC22A24	ENST00000326192.5 link	c.173C>G	p.Thr58Ser	missense_variant	1/4	1		ENSP00000321549.5	Q8N4F4-1

Frequencies

GnomAD3 genomes

AF:

0.761

AC:

115589

AN:

151964

Hom.:

45532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.799

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.773

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.843

Gnomad OTH

AF:

0.796

GnomAD3 exomes

AF:

0.836

AC:

180972

AN:

216350

Hom.:

76583

AF XY:

0.840

AC XY:

98060

AN XY:

116760

show subpopulations

Gnomad AFR exome

AF:

0.533

Gnomad AMR exome

AF:

0.894

Gnomad ASJ exome

AF:

0.776

Gnomad EAS exome

AF:

0.917

Gnomad SAS exome

AF:

0.829

Gnomad FIN exome

AF:

0.885

Gnomad NFE exome

AF:

0.847

Gnomad OTH exome

AF:

0.835

GnomAD4 exome

AF:

0.842

AC:

1197282

AN:

1422470

Hom.:

506064

Cov.:

AF XY:

0.842

AC XY:

594048

AN XY:

705606

show subpopulations

Gnomad4 AFR exome

AF:

0.531

Gnomad4 AMR exome

AF:

0.887

Gnomad4 ASJ exome

AF:

0.768

Gnomad4 EAS exome

AF:

0.907

Gnomad4 SAS exome

AF:

0.832

Gnomad4 FIN exome

AF:

0.885

Gnomad4 NFE exome

AF:

0.848

Gnomad4 OTH exome

AF:

0.823

GnomAD4 genome

AF:

0.760

AC:

115622

AN:

152082

Hom.:

45537

Cov.:

AF XY:

0.763

AC XY:

56729

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.536

Gnomad4 AMR

AF:

0.831

Gnomad4 ASJ

AF:

0.773

Gnomad4 EAS

AF:

0.902

Gnomad4 SAS

AF:

0.844

Gnomad4 FIN

AF:

0.882

Gnomad4 NFE

AF:

0.843

Gnomad4 OTH

AF:

0.789

Alfa

AF:

0.825

Hom.:

31661

Bravo

AF:

0.750

TwinsUK

AF:

0.845

AC:

3133

ALSPAC

AF:

0.851

AC:

3279

ESP6500AA

AF:

0.518

AC:

717

ESP6500EA

AF:

0.828

AC:

2635

ExAC

AF:

0.826

AC:

100132

Asia WGS

AF:

0.825

AC:

2866

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

0.0041

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.56

T;T;.

MetaRNN

Benign

9.1e-7

T;T;T

MetaSVM

Benign

-1.1

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-3.8

D;.;D

REVEL

Benign

0.086

Sift

Benign

0.12

T;.;T

Sift4G

Benign

0.19

T;T;T

Polyphen

1.0

D;.;.

Vest4

0.015

MutPred

0.40

Gain of disorder (P = 0.0571);Gain of disorder (P = 0.0571);Gain of disorder (P = 0.0571);

MPC

0.0090

ClinPred

0.051

GERP RS

2.3

gMVP

0.11

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over