Genetic Variant SLCO4C1:c.1469+77A>G (chr5-102257038-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_180991.5(SLCO4C1):c.1469+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 1,215,314 control chromosomes in the GnomAD database, including 237,779 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 ( 30714 hom., cov: 33)

Exomes 𝑓: 0.62 ( 207065 hom. )

Consequence

SLCO4C1
NM_180991.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.866

Publications

8 publications found

Variant links:

Genes affected

SLCO4C1 (HGNC:23612): (solute carrier organic anion transporter family member 4C1) SLCO4C1 belongs to the organic anion transporter (OATP) family. OATPs are involved in the membrane transport of bile acids, conjugated steroids, thyroid hormone, eicosanoids, peptides, and numerous drugs in many tissues (Mikkaichi et al., 2004 [PubMed 14993604]).[supplied by OMIM, Mar 2008]

SLCO4C1 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_180991.5. 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
	SLCO4C1	NM_180991.5	MANE Select	c.1469+77A>G		intron	N/A	NP_851322.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLCO4C1	ENST00000310954.7	TSL:1 MANE Select	c.1469+77A>G	intron	N/A	ENSP00000309741.6	Q6ZQN7
SLCO4C1	ENST00000893538.1		c.1469+77A>G	intron	N/A	ENSP00000563597.1
SLCO4C1	ENST00000893537.1		c.1205+77A>G	intron	N/A	ENSP00000563596.1

Frequencies

GnomAD3 genomes

AF:

0.634

AC:

96386

AN:

151996

Hom.:

30670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.554

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.635

Gnomad FIN

AF:

0.700

Gnomad MID

AF:

0.704

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.639

GnomAD4 exome

AF:

0.624

AC:

663048

AN:

1063200

Hom.:

207065

AF XY:

0.625

AC XY:

321286

AN XY:

513978

show subpopulations

African (AFR)

AF:

0.615

AC:

13767

AN:

22372

American (AMR)

AF:

0.599

AC:

9300

AN:

15532

Ashkenazi Jewish (ASJ)

AF:

0.582

AC:

8660

AN:

14876

East Asian (EAS)

AF:

0.683

AC:

20254

AN:

29664

South Asian (SAS)

AF:

0.643

AC:

18877

AN:

29374

European-Finnish (FIN)

AF:

0.696

AC:

28868

AN:

41500

Middle Eastern (MID)

AF:

0.677

AC:

2580

AN:

3810

European-Non Finnish (NFE)

AF:

0.618

AC:

533092

AN:

862878

Other (OTH)

AF:

0.640

AC:

27650

AN:

43194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

11734

23469

35203

46938

58672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15750

31500

47250

63000

78750

<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:

0.634

AC:

96480

AN:

152114

Hom.:

30714

Cov.:

AF XY:

0.636

AC XY:

47271

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.623

AC:

25836

AN:

41484

American (AMR)

AF:

0.635

AC:

9703

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

2061

AN:

3468

East Asian (EAS)

AF:

0.693

AC:

3584

AN:

5168

South Asian (SAS)

AF:

0.635

AC:

3063

AN:

4826

European-Finnish (FIN)

AF:

0.700

AC:

7396

AN:

10570

Middle Eastern (MID)

AF:

0.705

AC:

206

AN:

292

European-Non Finnish (NFE)

AF:

0.629

AC:

42769

AN:

67998

Other (OTH)

AF:

0.644

AC:

1359

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1832

3665

5497

7330

9162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.626

Hom.:

50229

Bravo

AF:

0.622

Asia WGS

AF:

0.675

AC:

2349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.7

(source)

DANN

Benign

0.79

PhyloP100

0.87

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