Genetic Variant SLC22A10:c.661+41T>G (chr11-63297498-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

Publications

12 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC22A10	NM_001039752.4 link	c.661+41T>G		intron_variant	Intron 3 of 9	ENST00000332793.11	NP_001034841.3	Q63ZE4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A10	ENST00000332793.11 link	c.661+41T>G		intron_variant	Intron 3 of 9	1	NM_001039752.4	ENSP00000327569.6		Q63ZE4-1

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100407

AN:

151868

Hom.:

33558

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.611

AC:

151277

AN:

247458

AF XY:

0.608

show subpopulations

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 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.:

AF XY:

0.643

AC XY:

466265

AN XY:

724814

show subpopulations

African (AFR)

AF:

0.739

AC:

24578

AN:

33280

American (AMR)

AF:

0.560

AC:

24816

AN:

44320

Ashkenazi Jewish (ASJ)

AF:

0.529

AC:

13790

AN:

26044

East Asian (EAS)

AF:

0.413

AC:

16360

AN:

39636

South Asian (SAS)

AF:

0.494

AC:

42330

AN:

85772

European-Finnish (FIN)

AF:

0.654

AC:

34924

AN:

53364

Middle Eastern (MID)

AF:

0.607

AC:

3488

AN:

5742

European-Non Finnish (NFE)

AF:

0.672

AC:

746061

AN:

1109638

Other (OTH)

AF:

0.639

AC:

38484

AN:

60214

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

19122

38243

57365

76486

95608

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19118

38236

57354

76472

95590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.661

AC:

100499

AN:

151986

Hom.:

33595

Cov.:

AF XY:

0.653

AC XY:

48485

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.743

AC:

30788

AN:

41444

American (AMR)

AF:

0.593

AC:

9051

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1870

AN:

3470

East Asian (EAS)

AF:

0.435

AC:

2247

AN:

5164

South Asian (SAS)

AF:

0.487

AC:

2345

AN:

4818

European-Finnish (FIN)

AF:

0.635

AC:

6698

AN:

10540

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.669

AC:

45455

AN:

67978

Other (OTH)

AF:

0.639

AC:

1346

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1693

3385

5078

6770

8463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.657

Hom.:

58982

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

(source)

DANN

Benign

0.45

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over