rs1944043

Positions:

• chr11-63096394-A-C
• chr11-63096394-A-G
• chr11-63096394-A-T

Variant summary

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

The NM_001136506.2(SLC22A24):​c.955-288T>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 152,122 control chromosomes in the GnomAD database, including 44,791 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 (44791 hom., cov: 32)
• Consequence: SLC22A24 NM_001136506.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A24	NM_001136506.2	c.955-288T>G		intron_variant		ENST00000612278.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A24	ENST00000612278.4	c.955-288T>G		intron_variant		5	NM_001136506.2	P4
SLC22A24	ENST00000417740.5	c.955-288T>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115681 AN: 152004 Hom.: 44779 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.820

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: 115727 AN: 152122 Hom.: 44791 Cov.: 32 AF XY: 0.764 AC XY: 56817 AN XY: 74362

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.787

Alfa AF: 0.769 Hom.: 5621

Bravo AF: 0.754

Asia WGS AF: 0.822 AC: 2858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.73

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: rs1944043; hg19: chr11-62863866;