5-102284470-T-C

Variant names:

• chr5-102284470-T-C
• rs2548724
• NM_180991.5:c.619+6873A>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+6873A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,104 control chromosomes in the GnomAD database, including 50,521 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 0.81 (50521 hom., cov: 31)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 13 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.619+6873A>G		intron_variant	Intron 2 of 12	ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.355+11438A>G		intron_variant	Intron 1 of 11		XP_011541672.1
SLCO4C1	XM_011543372.2	c.205+6873A>G		intron_variant	Intron 4 of 14		XP_011541674.1
SLCO4C1	XM_047417146.1	c.205+6873A>G		intron_variant	Intron 4 of 14		XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.619+6873A>G		intron_variant	Intron 2 of 12	1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123079 AN: 151986 Hom.: 50463 Cov.: 31

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.810 AC: 123197 AN: 152104 Hom.: 50521 Cov.: 31 AF XY: 0.807 AC XY: 60041 AN XY: 74368

African (AFR) AF: 0.943 AC: 39150 AN: 41526

American (AMR) AF: 0.809 AC: 12358 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2658 AN: 3466

East Asian (EAS) AF: 0.710 AC: 3670 AN: 5172

South Asian (SAS) AF: 0.707 AC: 3411 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8183 AN: 10592

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51142 AN: 67930

Other (OTH) AF: 0.831 AC: 1756 AN: 2112

Alfa AF: 0.771 Hom.: 83064

Bravo AF: 0.818

Asia WGS AF: 0.744 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2548724; hg19: chr5-101620174;