rs709369

chr5-102288632-T-Cchr5-102288632-T-G

Variant summary

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

The NM_180991.5(SLCO4C1):c.619+2711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,022 control chromosomes in the GnomAD database, including 19,470 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 0.49 (19470 hom., cov: 32)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO4C1	NM_180991.5	c.619+2711A>G		intron_variant		ENST00000310954.7
SLCO4C1	XM_011543370.3	c.355+7276A>G		intron_variant
SLCO4C1	XM_011543372.2	c.205+2711A>G		intron_variant
SLCO4C1	XM_047417146.1	c.205+2711A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.619+2711A>G		intron_variant		1	NM_180991.5	P1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74357 AN: 151904 Hom.: 19430 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.490 AC: 74447 AN: 152022 Hom.: 19470 Cov.: 32 AF XY: 0.483 AC XY: 35930 AN XY: 74316

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.496

Alfa AF: 0.427 Hom.: 18441

Bravo AF: 0.514

Asia WGS AF: 0.534 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.66

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: rs709369; hg19: chr5-101624336;