dbSNP rs1404608: SLC22A10:c.*480T>C (chr11-63311514-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.*480T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,208 control chromosomes in the GnomAD database, including 18,269 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 ( 18244 hom., cov: 32)

Exomes 𝑓: 0.48 ( 25 hom. )

Consequence

SLC22A10
NM_001039752.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.554

Publications

8 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 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.*480T>C		3_prime_UTR	Exon 10 of 10	NP_001034841.3	Q63ZE4-1
	SLC22A10	NR_134874.2		n.1974T>C		non_coding_transcript_exon	Exon 11 of 11

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC22A10	ENST00000332793.11	TSL:1 MANE Select	c.*480T>C	3_prime_UTR	Exon 10 of 10	ENSP00000327569.6	Q63ZE4-1
SLC22A10	ENST00000533483.5	TSL:1	n.*692T>C	non_coding_transcript_exon	Exon 11 of 11	ENSP00000433048.1	E9PMM0
SLC22A10	ENST00000533483.5	TSL:1	n.*692T>C	3_prime_UTR	Exon 11 of 11	ENSP00000433048.1	E9PMM0

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71526

AN:

151922

Hom.:

18253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.598

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.485

GnomAD4 exome

AF:

0.476

AC:

AN:

170

Hom.:

Cov.:

AF XY:

0.509

AC XY:

AN XY:

106

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.479

AC:

AN:

144

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.470

AC:

71516

AN:

152038

Hom.:

18244

Cov.:

AF XY:

0.470

AC XY:

34934

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.262

AC:

10871

AN:

41462

American (AMR)

AF:

0.499

AC:

7623

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.436

AC:

1513

AN:

3472

East Asian (EAS)

AF:

0.433

AC:

2242

AN:

5180

South Asian (SAS)

AF:

0.455

AC:

2192

AN:

4820

European-Finnish (FIN)

AF:

0.598

AC:

6302

AN:

10546

Middle Eastern (MID)

AF:

0.455

AC:

133

AN:

292

European-Non Finnish (NFE)

AF:

0.576

AC:

39152

AN:

67968

Other (OTH)

AF:

0.480

AC:

1013

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1799

3598

5398

7197

8996

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<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:

0.537

Hom.:

60902

Bravo

AF:

0.457

Asia WGS

AF:

0.455

AC:

1577

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.8

(source)

DANN

Benign

0.25

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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