rs972505

chr12-20750301-C-Achr12-20750301-C-Gchr12-20750301-C-T

Variant summary

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

The NM_017435.5(SLCO1C1):c.1799-374C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,808 control chromosomes in the GnomAD database, including 17,775 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 0.46 (17775 hom., cov: 32)
• Consequence: SLCO1C1 NM_017435.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

SLCO1C1 (HGNC:13819): (solute carrier organic anion transporter family member 1C1) This gene encodes a member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of thyroid hormones in brain tissues. This protein has particularly high affinity for the thyroid hormones thyroxine, tri-iodothyronine and reverse tri-iodothyronine. Polymorphisms in the gene encoding this protein may be associated with fatigue and depression in patients suffering from hyperthyroidism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO1C1	NM_017435.5	c.1799-374C>A		intron_variant		ENST00000266509.7
SLCO1C1	NM_001145944.2	c.1445-374C>A		intron_variant
SLCO1C1	NM_001145945.2	c.1652-374C>A		intron_variant
SLCO1C1	NM_001145946.2	c.1799-374C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO1C1	ENST00000266509.7	c.1799-374C>A		intron_variant		1	NM_017435.5	P1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69534 AN: 151690 Hom.: 17773 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.458 AC: 69547 AN: 151808 Hom.: 17775 Cov.: 32 AF XY: 0.462 AC XY: 34237 AN XY: 74182

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.448

Alfa AF: 0.533 Hom.: 42370

Bravo AF: 0.456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.020
Dann	Benign	0.37

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: rs972505; hg19: chr12-20903235;