chr5-102257038-T-C

Position:

• chr5-102257038-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.1469+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 1,215,314 control chromosomes in the GnomAD database, including 237,779 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 0.63 (30714 hom., cov: 33)
  • Exomes 𝑓: 0.62 (207065 hom.)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.1469+77A>G		intron_variant		ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.1205+77A>G		intron_variant			XP_011541672.1
SLCO4C1	XM_011543372.2	c.1055+77A>G		intron_variant			XP_011541674.1
SLCO4C1	XM_047417146.1	c.1055+77A>G		intron_variant			XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.1469+77A>G		intron_variant		1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96386 AN: 151996 Hom.: 30670 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.639

GnomAD4 exome AF: 0.624 AC: 663048 AN: 1063200 Hom.: 207065 AF XY: 0.625 AC XY: 321286 AN XY: 513978

Gnomad4 AFR exome AF: 0.615

Gnomad4 AMR exome AF: 0.599

Gnomad4 ASJ exome AF: 0.582

Gnomad4 EAS exome AF: 0.683

Gnomad4 SAS exome AF: 0.643

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.618

Gnomad4 OTH exome AF: 0.640

GnomAD4 genome AF: 0.634 AC: 96480 AN: 152114 Hom.: 30714 Cov.: 33 AF XY: 0.636 AC XY: 47271 AN XY: 74350

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.644

Alfa AF: 0.627 Hom.: 39846

Bravo AF: 0.622

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.79

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: rs174414; hg19: chr5-101592742;