5-102234532-T-C

Variant names:

• chr5-102234532-T-C
• rs3811976
• NM_180991.5:c.*2326A>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.*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
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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.*2326A>G		3_prime_UTR	Exon 13 of 13	NP_851322.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO4C1	ENST00000310954.7	TSL:1 MANE Select	c.*2326A>G		3_prime_UTR	Exon 13 of 13	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0938 AC: 27 AN: 288

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.105 AC: 4378 AN: 41560

American (AMR) AF: 0.0494 AC: 756 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3470

East Asian (EAS) AF: 0.0657 AC: 340 AN: 5172

South Asian (SAS) AF: 0.0840 AC: 406 AN: 4832

European-Finnish (FIN) AF: 0.111 AC: 1181 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5983 AN: 68000

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0848 Hom.: 2268

Bravo AF: 0.0830

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.35
PhyloP100		-1.8
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: rs3811976; hg19: chr5-101570236;