11-63199905-T-C

Variant names:

• chr11-63199905-T-C
• rs1525064
• NM_199352.6:c.831-16088A>G

Variant summary

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

The NM_199352.6(SLC22A25):​c.831-16088A>G variant causes a intron change. The variant allele was found at a frequency of 0.49 in 151,588 control chromosomes in the GnomAD database, including 19,166 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 0.49 (19166 hom., cov: 28)
• Consequence: SLC22A25 NM_199352.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 5 publications found

Genes affected

SLC22A25 (HGNC:32935): (solute carrier family 22 member 25) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A25	NM_199352.6	c.831-16088A>G		intron_variant	Intron 7 of 11	ENST00000306494.11	NP_955384.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A25	ENST00000306494.11	c.831-16088A>G		intron_variant	Intron 7 of 11	1	NM_199352.6	ENSP00000307443.6
SLC22A25	ENST00000525295.1	n.403-16088A>G		intron_variant	Intron 1 of 6	1		ENSP00000435614.1
SLC22A25	ENST00000527057.5	n.825-16088A>G		intron_variant	Intron 4 of 9	1		ENSP00000432242.1
SLC22A25	ENST00000528239.5	n.*480-16088A>G		intron_variant	Intron 6 of 10	1		ENSP00000431235.1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74309 AN: 151470 Hom.: 19175 Cov.: 28

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.490 AC: 74315 AN: 151588 Hom.: 19166 Cov.: 28 AF XY: 0.491 AC XY: 36351 AN XY: 74012

African (AFR) AF: 0.331 AC: 13684 AN: 41316

American (AMR) AF: 0.501 AC: 7604 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1504 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2229 AN: 5132

South Asian (SAS) AF: 0.459 AC: 2190 AN: 4774

European-Finnish (FIN) AF: 0.642 AC: 6751 AN: 10508

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38716 AN: 67910

Other (OTH) AF: 0.495 AC: 1038 AN: 2096

Alfa AF: 0.521 Hom.: 2771

Bravo AF: 0.475

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.35
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: rs1525064; hg19: chr11-62967377;