chr11-63139576-A-C

Position:

• chr11-63139576-A-C

Variant summary

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

The NM_001136506.2(SLC22A24):​c.402+3802T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,032 control chromosomes in the GnomAD database, including 45,502 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 (45502 hom., cov: 31)
• Consequence: SLC22A24 NM_001136506.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

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=-1.01).
• 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	c.402+3802T>G		intron_variant		ENST00000612278.4	NP_001129978.2
SLC22A24	NM_173586.3	c.402+3802T>G		intron_variant			NP_775857.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A24	ENST00000612278.4	c.402+3802T>G		intron_variant		5	NM_001136506.2	ENSP00000480336	P4
SLC22A24	ENST00000326192.5	c.402+3802T>G		intron_variant		1		ENSP00000321549
SLC22A24	ENST00000417740.5	c.402+3802T>G		intron_variant		5		ENSP00000396586	A1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115528 AN: 151914 Hom.: 45497 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.760 AC: 115561 AN: 152032 Hom.: 45502 Cov.: 31 AF XY: 0.763 AC XY: 56691 AN XY: 74300

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.789

Alfa AF: 0.737 Hom.: 2411

Bravo AF: 0.752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.44

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: rs7948969; hg19: chr11-62907048; COSMIC: COSV58224867;