rs1404608

Positions:

• chr11-63311514-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.*480T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,208 control chromosomes in the GnomAD database, including 18,269 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 0.47 (18244 hom., cov: 32)
  • Exomes 𝑓: 0.48 (25 hom.)
• Consequence: SLC22A10 NM_001039752.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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]

SLC22A10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A10	NM_001039752.4	c.*480T>C		3_prime_UTR_variant	10/10	ENST00000332793.11	NP_001034841.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A10	ENST00000332793.11	c.*480T>C		3_prime_UTR_variant	10/10	1	NM_001039752.4	ENSP00000327569.6
SLC22A10	ENST00000533483.5	n.*692T>C		non_coding_transcript_exon_variant	11/11	1		ENSP00000433048.1
SLC22A10	ENST00000533483.5	n.*692T>C		3_prime_UTR_variant	11/11	1		ENSP00000433048.1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71526 AN: 151922 Hom.: 18253 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.476 AC: 81 AN: 170 Hom.: 25 Cov.: 0 AF XY: 0.509 AC XY: 54 AN XY: 106

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.250

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.479

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.470 AC: 71516 AN: 152038 Hom.: 18244 Cov.: 32 AF XY: 0.470 AC XY: 34934 AN XY: 74320

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.480

Alfa AF: 0.553 Hom.: 41756

Bravo AF: 0.457

Asia WGS AF: 0.455 AC: 1577 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1404608; hg19: chr11-63078986;