rs515213

chr11-63299431-T-C

Variant summary

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

The NM_001039752.4(SLC22A10):c.955-83T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,099,846 control chromosomes in the GnomAD database, including 213,060 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 0.63 (30198 hom., cov: 31)
  • Exomes 𝑓: 0.62 (182862 hom.)
• Consequence: SLC22A10 NM_001039752.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

SLC22A10 (HGNC:18057): (solute carrier family 22 member 10) 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A10	NM_001039752.4	c.955-83T>C		intron_variant		ENST00000332793.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A10	ENST00000332793.11	c.955-83T>C		intron_variant		1	NM_001039752.4	P1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95324 AN: 151836 Hom.: 30170 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.609

GnomAD4 exome AF: 0.617 AC: 585024 AN: 947892 Hom.: 182862 AF XY: 0.613 AC XY: 297578 AN XY: 485678

Gnomad4 AFR exome AF: 0.678

Gnomad4 AMR exome AF: 0.550

Gnomad4 ASJ exome AF: 0.462

Gnomad4 EAS exome AF: 0.412

Gnomad4 SAS exome AF: 0.494

Gnomad4 FIN exome AF: 0.640

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.611

GnomAD4 genome AF: 0.628 AC: 95405 AN: 151954 Hom.: 30198 Cov.: 31 AF XY: 0.621 AC XY: 46152 AN XY: 74270

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.607

Alfa AF: 0.633 Hom.: 30958

Bravo AF: 0.629

Asia WGS AF: 0.518 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.1
Dann	Benign	0.48

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: rs515213; hg19: chr11-63066903; COSMIC: COSV60421666;