dbSNP rs515213: SLC22A10:c.955-83T>C (chr11-63299431-T-C) – 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.955-83T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,099,846 control chromosomes in the GnomAD database, including 213,060 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 0.63 ( 30198 hom., cov: 31)

Exomes 𝑓: 0.62 ( 182862 hom. )

Consequence

SLC22A10
NM_001039752.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

6 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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.955-83T>C		intron	N/A	NP_001034841.3	Q63ZE4-1
	SLC22A10	NR_134874.2		n.962-83T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC22A10	ENST00000332793.11	TSL:1 MANE Select	c.955-83T>C	intron	N/A	ENSP00000327569.6	Q63ZE4-1
SLC22A10	ENST00000532724.5	TSL:1	n.498-83T>C	intron	N/A
SLC22A10	ENST00000533483.5	TSL:1	n.799-83T>C	intron	N/A	ENSP00000433048.1	E9PMM0

Frequencies

GnomAD3 genomes

AF:

0.628

AC:

95324

AN:

151836

Hom.:

30170

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.574

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.643

Gnomad OTH

AF:

0.609

GnomAD4 exome

AF:

0.617

AC:

585024

AN:

947892

Hom.:

182862

AF XY:

0.613

AC XY:

297578

AN XY:

485678

show subpopulations

African (AFR)

AF:

0.678

AC:

15891

AN:

23426

American (AMR)

AF:

0.550

AC:

20254

AN:

36840

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

10027

AN:

21704

East Asian (EAS)

AF:

0.412

AC:

14758

AN:

35834

South Asian (SAS)

AF:

0.494

AC:

34522

AN:

69934

European-Finnish (FIN)

AF:

0.640

AC:

32312

AN:

50452

Middle Eastern (MID)

AF:

0.550

AC:

2639

AN:

4800

European-Non Finnish (NFE)

AF:

0.647

AC:

428311

AN:

661846

Other (OTH)

AF:

0.611

AC:

26310

AN:

43056

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

10822

21645

32467

43290

54112

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8890

17780

26670

35560

44450

<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:

0.628

AC:

95405

AN:

151954

Hom.:

30198

Cov.:

AF XY:

0.621

AC XY:

46152

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.681

AC:

28219

AN:

41428

American (AMR)

AF:

0.574

AC:

8752

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

1634

AN:

3472

East Asian (EAS)

AF:

0.436

AC:

2249

AN:

5162

South Asian (SAS)

AF:

0.488

AC:

2350

AN:

4818

European-Finnish (FIN)

AF:

0.623

AC:

6578

AN:

10556

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.643

AC:

43669

AN:

67960

Other (OTH)

AF:

0.607

AC:

1278

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1794

3588

5382

7176

8970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.633

Hom.:

45041

Bravo

AF:

0.629

Asia WGS

AF:

0.518

AC:

1804

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.1

(source)

DANN

Benign

0.48

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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