rs1525064

Positions:

• chr11-63199905-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC22A25	NM_199352.6	c.831-16088A>G		intron_variant		ENST00000306494.11	NP_955384.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A25	ENST00000306494.11	c.831-16088A>G		intron_variant		1	NM_199352.6	ENSP00000307443.6
SLC22A25	ENST00000525295.1	n.403-16088A>G		intron_variant		1		ENSP00000435614.1
SLC22A25	ENST00000527057.5	n.825-16088A>G		intron_variant		1		ENSP00000432242.1
SLC22A25	ENST00000528239.5	n.*480-16088A>G		intron_variant		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

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.495

Alfa AF: 0.528 Hom.: 2723

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

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: rs1525064; hg19: chr11-62967377;