Genetic Variant SLC22A9:c.403-125G>A (chr11-63371010-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_080866.3(SLC22A9):c.403-125G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 641,576 control chromosomes in the GnomAD database, including 119,343 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 0.61 ( 28774 hom., cov: 32)

Exomes 𝑓: 0.60 ( 90569 hom. )

Consequence

SLC22A9
NM_080866.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

12 publications found

Variant links:

Genes affected

SLC22A9 (HGNC:16261): (solute carrier family 22 member 9) Enables anion:anion antiporter activity; short-chain fatty acid transmembrane transporter activity; and sodium-independent organic anion transmembrane transporter activity. Involved in hormone transport; short-chain fatty acid import; and sodium-independent organic anion transport. Located in basolateral plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC22A9 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC22A9	NM_080866.3 link	c.403-125G>A	intron_variant	Intron 1 of 9	ENST00000279178.4	NP_543142.2	Q8IVM8-1
SLC22A9	XM_017017159.3 link	c.403-125G>A	intron_variant	Intron 1 of 7		XP_016872648.1
SLC22A9	XM_047426335.1 link	c.-261G>A	upstream_gene_variant			XP_047282291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4 link	c.403-125G>A		intron_variant	Intron 1 of 9	1	NM_080866.3	ENSP00000279178.3		Q8IVM8-1
SLC22A9	ENST00000536333.5 link	n.403-125G>A		intron_variant	Intron 1 of 6	1		ENSP00000440206.1		Q8IVM8-2

Frequencies

GnomAD3 genomes

AF:

0.613

AC:

93157

AN:

151880

Hom.:

28745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.642

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.618

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.592

GnomAD4 exome

AF:

0.603

AC:

294978

AN:

489576

Hom.:

90569

AF XY:

0.597

AC XY:

153118

AN XY:

256342

show subpopulations

African (AFR)

AF:

0.636

AC:

7982

AN:

12542

American (AMR)

AF:

0.537

AC:

9594

AN:

17864

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

6180

AN:

13110

East Asian (EAS)

AF:

0.408

AC:

12143

AN:

29796

South Asian (SAS)

AF:

0.471

AC:

19166

AN:

40676

European-Finnish (FIN)

AF:

0.634

AC:

23614

AN:

37232

Middle Eastern (MID)

AF:

0.529

AC:

1898

AN:

3588

European-Non Finnish (NFE)

AF:

0.644

AC:

198255

AN:

308014

Other (OTH)

AF:

0.603

AC:

16146

AN:

26754

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5368

10736

16105

21473

26841

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1974

3948

5922

7896

9870

<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:

0.613

AC:

93238

AN:

152000

Hom.:

28774

Cov.:

AF XY:

0.608

AC XY:

45157

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.642

AC:

26628

AN:

41446

American (AMR)

AF:

0.566

AC:

8635

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1682

AN:

3472

East Asian (EAS)

AF:

0.433

AC:

2240

AN:

5168

South Asian (SAS)

AF:

0.472

AC:

2275

AN:

4818

European-Finnish (FIN)

AF:

0.618

AC:

6540

AN:

10574

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.637

AC:

43321

AN:

67958

Other (OTH)

AF:

0.590

AC:

1243

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1854

3708

5562

7416

9270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.627

Hom.:

47483

Bravo

AF:

0.613

Asia WGS

AF:

0.510

AC:

1775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.12

(source)

DANN

Benign

0.33

PhyloP100

-1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over