5-102259854-C-T

Position:

• chr5-102259854-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_180991.5(SLCO4C1):​c.1128+359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 151,970 control chromosomes in the GnomAD database, including 43,064 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 0.75 (43064 hom., cov: 31)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.1128+359G>A		intron_variant		ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.864+359G>A		intron_variant			XP_011541672.1
SLCO4C1	XM_011543372.2	c.714+359G>A		intron_variant			XP_011541674.1
SLCO4C1	XM_047417146.1	c.714+359G>A		intron_variant			XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.1128+359G>A		intron_variant		1	NM_180991.5	ENSP00000309741	P1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114233 AN: 151852 Hom.: 43021 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.752 AC: 114330 AN: 151970 Hom.: 43064 Cov.: 31 AF XY: 0.752 AC XY: 55882 AN XY: 74262

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.784

Alfa AF: 0.743 Hom.: 9675

Bravo AF: 0.752

Asia WGS AF: 0.727 AC: 2526 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.7
DANN	Benign	0.14

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

LitVar

Other links and lift over

dbSNP: rs370176; hg19: chr5-101595558;