chr5-102234532-T-C

Position:

• chr5-102234532-T-C

Variant summary

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

The NM_180991.5(SLCO4C1):​c.*2326A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,546 control chromosomes in the GnomAD database, including 637 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 0.088 (635 hom., cov: 33)
  • Exomes 𝑓: 0.092 (2 hom.)
• Consequence: SLCO4C1 NM_180991.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.*2326A>G		3_prime_UTR_variant	13/13	ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.*2326A>G		3_prime_UTR_variant	12/12		XP_011541672.1
SLCO4C1	XM_011543372.2	c.*2326A>G		3_prime_UTR_variant	15/15		XP_011541674.1
SLCO4C1	XM_047417146.1	c.*2326A>G		3_prime_UTR_variant	15/15		XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954	c.*2326A>G		3_prime_UTR_variant	13/13	1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13427 AN: 152134 Hom.: 635 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.0645

GnomAD4 exome AF: 0.0918 AC: 27 AN: 294 Hom.: 2 Cov.: 0 AF XY: 0.0928 AC XY: 18 AN XY: 194

Gnomad4 FIN exome AF: 0.0938

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0882 AC: 13432 AN: 152252 Hom.: 635 Cov.: 33 AF XY: 0.0897 AC XY: 6675 AN XY: 74440

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.0840

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0828 Hom.: 1090

Bravo AF: 0.0830

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.35

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: rs3811976; hg19: chr5-101570236;