5-102239683-G-C

Variant names:

• chr5-102239683-G-C
• rs6596425
• NM_180991.5:c.1877-295C>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.1877-295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,688 control chromosomes in the GnomAD database, including 5,551 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 0.25 (5551 hom., cov: 32)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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.1877-295C>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.1877-295C>G		intron	N/A	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38182 AN: 151572 Hom.: 5545 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.252 AC: 38220 AN: 151688 Hom.: 5551 Cov.: 32 AF XY: 0.253 AC XY: 18741 AN XY: 74110

African (AFR) AF: 0.407 AC: 16844 AN: 41380

American (AMR) AF: 0.203 AC: 3090 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5150

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4812

European-Finnish (FIN) AF: 0.175 AC: 1845 AN: 10542

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11923 AN: 67816

Other (OTH) AF: 0.208 AC: 436 AN: 2096

Alfa AF: 0.210 Hom.: 478

Bravo AF: 0.259

Asia WGS AF: 0.292 AC: 1006 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.71
PhyloP100		-2.2
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: rs6596425; hg19: chr5-101575387; COSMIC: COSV60514027;