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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039752.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A10	NM_001039752.4	MANE Select	c.661+41T>G		intron	N/A	NP_001034841.3	Q63ZE4-1
	SLC22A10	NR_134874.2		n.668+41T>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC22A10	ENST00000332793.11	TSL:1 MANE Select	c.661+41T>G	intron	N/A	ENSP00000327569.6	Q63ZE4-1
SLC22A10	ENST00000532724.5	TSL:1	n.374-1422T>G	intron	N/A
SLC22A10	ENST00000533483.5	TSL:1	n.505+41T>G	intron	N/A	ENSP00000433048.1	E9PMM0

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over