rs11231379

Variant names:

• chr11-63137463-C-G
• rs11231379
• NM_001136506.2:c.403-2695G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136506.2(SLC22A24):​c.403-2695G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,160 control chromosomes in the GnomAD database, including 1,240 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1240 hom., cov: 32)
• Consequence: SLC22A24 NM_001136506.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A24	NM_001136506.2	c.403-2695G>C		intron_variant	Intron 1 of 9	ENST00000612278.4	NP_001129978.2
SLC22A24	NM_173586.3	c.403-2695G>C		intron_variant	Intron 1 of 3		NP_775857.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A24	ENST00000612278.4	c.403-2695G>C		intron_variant	Intron 1 of 9	5	NM_001136506.2	ENSP00000480336.1
SLC22A24	ENST00000417740.5	c.403-2695G>C		intron_variant	Intron 1 of 9	5		ENSP00000396586.1
SLC22A24	ENST00000326192.5	c.403-2695G>C		intron_variant	Intron 1 of 3	1		ENSP00000321549.5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18288 AN: 152042 Hom.: 1237 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 18304 AN: 152160 Hom.: 1240 Cov.: 32 AF XY: 0.121 AC XY: 9016 AN XY: 74386

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0951

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.115

Alfa AF: 0.131 Hom.: 172

Bravo AF: 0.116

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs11231379; hg19: chr11-62904935;