11-63269395-C-T

Variant names:

• chr11-63269395-C-T
• rs1944086
• ENST00000682643.1:c.-307+470C>T

Variant summary

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

The ENST00000682643.1(SLC22A10):​c.-307+470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,056 control chromosomes in the GnomAD database, including 18,304 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 (18304 hom., cov: 31)
• Consequence: SLC22A10 ENST00000682643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A10	ENST00000682643.1	c.-307+470C>T		intron_variant	Intron 1 of 6			ENSP00000506810.1
SLC22A10	ENST00000525620.2	n.669+470C>T		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71623 AN: 151938 Hom.: 18312 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.471 AC: 71615 AN: 152056 Hom.: 18304 Cov.: 31 AF XY: 0.471 AC XY: 34993 AN XY: 74326

African (AFR) AF: 0.263 AC: 10899 AN: 41494

American (AMR) AF: 0.499 AC: 7616 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2250 AN: 5156

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4816

European-Finnish (FIN) AF: 0.598 AC: 6324 AN: 10572

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39189 AN: 67962

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.518 Hom.: 2595

Bravo AF: 0.457

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.68
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1944086; hg19: chr11-63036867;