rs709369

Variant names:

• chr5-102288632-T-C
• rs709369
• NM_180991.5:c.619+2711A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-102288632-T-C
• chr5-102288632-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_180991.5(SLCO4C1):​c.619+2711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,022 control chromosomes in the GnomAD database, including 19,470 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 0.49 (19470 hom., cov: 32)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO4C1	NM_180991.5	MANE Select	c.619+2711A>G		intron	N/A	NP_851322.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO4C1	ENST00000310954.7	TSL:1 MANE Select	c.619+2711A>G		intron	N/A	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74357 AN: 151904 Hom.: 19430 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.490 AC: 74447 AN: 152022 Hom.: 19470 Cov.: 32 AF XY: 0.483 AC XY: 35930 AN XY: 74316

African (AFR) AF: 0.672 AC: 27863 AN: 41436

American (AMR) AF: 0.531 AC: 8113 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2886 AN: 5164

South Asian (SAS) AF: 0.455 AC: 2192 AN: 4822

European-Finnish (FIN) AF: 0.285 AC: 3012 AN: 10580

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27512 AN: 67970

Other (OTH) AF: 0.496 AC: 1045 AN: 2108

Alfa AF: 0.437 Hom.: 24725

Bravo AF: 0.514

Asia WGS AF: 0.534 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs709369; hg19: chr5-101624336;