11-63297498-T-G

Position:

• chr11-63297498-T-G

Variant summary

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

The NM_001039752.4(SLC22A10):​c.661+41T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 1,609,996 control chromosomes in the GnomAD database, including 343,123 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 0.66 (33595 hom., cov: 31)
  • Exomes 𝑓: 0.65 (309528 hom.)
• Consequence: SLC22A10 NM_001039752.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A10	NM_001039752.4	c.661+41T>G		intron_variant		ENST00000332793.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A10	ENST00000332793.11	c.661+41T>G		intron_variant		1	NM_001039752.4	P1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100407 AN: 151868 Hom.: 33558 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.641

GnomAD3 exomes AF: 0.611 AC: 151277 AN: 247458 Hom.: 47280 AF XY: 0.608 AC XY: 81573 AN XY: 134202

Gnomad AFR exome AF: 0.747

Gnomad AMR exome AF: 0.560

Gnomad ASJ exome AF: 0.544

Gnomad EAS exome AF: 0.422

Gnomad SAS exome AF: 0.488

Gnomad FIN exome AF: 0.648

Gnomad NFE exome AF: 0.670

Gnomad OTH exome AF: 0.624

GnomAD4 exome AF: 0.648 AC: 944831 AN: 1458010 Hom.: 309528 Cov.: 42 AF XY: 0.643 AC XY: 466265 AN XY: 724814

Gnomad4 AFR exome AF: 0.739

Gnomad4 AMR exome AF: 0.560

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.413

Gnomad4 SAS exome AF: 0.494

Gnomad4 FIN exome AF: 0.654

Gnomad4 NFE exome AF: 0.672

Gnomad4 OTH exome AF: 0.639

GnomAD4 genome AF: 0.661 AC: 100499 AN: 151986 Hom.: 33595 Cov.: 31 AF XY: 0.653 AC XY: 48485 AN XY: 74294

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.639

Alfa AF: 0.654 Hom.: 41663

Bravo AF: 0.665

Asia WGS AF: 0.523 AC: 1821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs575009; hg19: chr11-63064970; COSMIC: COSV60421943;