rs7948969

Variant names:

• chr11-63139576-A-C
• rs7948969
• NM_001136506.2:c.402+3802T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-63139576-A-C
• chr11-63139576-A-G
• chr11-63139576-A-T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-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 rank	MANE	Protein	UniProt
SLC22A24	NM_001136506.2	c.402+3802T>G		intron_variant	Intron 1 of 9	ENST00000612278.4	NP_001129978.2
SLC22A24	NM_173586.3	c.402+3802T>G		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.402+3802T>G		intron_variant	Intron 1 of 9	5	NM_001136506.2	ENSP00000480336.1
SLC22A24	ENST00000417740.5	c.402+3802T>G		intron_variant	Intron 1 of 9	5		ENSP00000396586.1
SLC22A24	ENST00000326192.5	c.402+3802T>G		intron_variant	Intron 1 of 3	1		ENSP00000321549.5

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

African (AFR) AF: 0.536 AC: 22198 AN: 41414

American (AMR) AF: 0.831 AC: 12696 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2684 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4672 AN: 5180

South Asian (SAS) AF: 0.842 AC: 4056 AN: 4816

European-Finnish (FIN) AF: 0.881 AC: 9315 AN: 10570

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.843 AC: 57327 AN: 67982

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.717 Hom.: 2512

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
PhyloP100		-2.1
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: rs7948969; hg19: chr11-62907048; COSMIC: COSV58224867;