chr11-63096532-T-C

Variant names:

• chr11-63096532-T-C
• rs1944042
• NM_001136506.2:c.955-426A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136506.2(SLC22A24):​c.955-426A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,118 control chromosomes in the GnomAD database, including 44,808 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 0.76 (44808 hom., cov: 33)
• Consequence: SLC22A24 NM_001136506.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136506.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A24	NM_001136506.2	MANE Select	c.955-426A>G		intron	N/A	NP_001129978.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A24	ENST00000612278.4	TSL:5 MANE Select	c.955-426A>G		intron	N/A	ENSP00000480336.1
	SLC22A24	ENST00000417740.5	TSL:5	c.955-426A>G		intron	N/A	ENSP00000396586.1
	SLC22A24	ENST00000908490.1		c.403-426A>G		intron	N/A	ENSP00000578549.1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115690 AN: 152000 Hom.: 44795 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.761 AC: 115737 AN: 152118 Hom.: 44808 Cov.: 33 AF XY: 0.764 AC XY: 56824 AN XY: 74368

African (AFR) AF: 0.613 AC: 25415 AN: 41478

American (AMR) AF: 0.823 AC: 12552 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4683 AN: 5186

South Asian (SAS) AF: 0.821 AC: 3959 AN: 4820

European-Finnish (FIN) AF: 0.874 AC: 9263 AN: 10600

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54663 AN: 67988

Other (OTH) AF: 0.788 AC: 1665 AN: 2114

Alfa AF: 0.762 Hom.: 5758

Bravo AF: 0.754

Asia WGS AF: 0.822 AC: 2859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		0.89
Mutation Taster		=100/0	polymorphism (auto)

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: rs1944042; hg19: chr11-62864004;