5-102247951-G-C

Variant names:

• chr5-102247951-G-C
• rs10515323
• NM_180991.5:c.1621-509C>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.1621-509C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 119,750 control chromosomes in the GnomAD database, including 1,273 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 0.15 (1273 hom., cov: 25)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.1621-509C>G		intron_variant	Intron 9 of 12	ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.1357-509C>G		intron_variant	Intron 8 of 11		XP_011541672.1
SLCO4C1	XM_011543372.2	c.1207-509C>G		intron_variant	Intron 11 of 14		XP_011541674.1
SLCO4C1	XM_047417146.1	c.1207-509C>G		intron_variant	Intron 11 of 14		XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.1621-509C>G		intron_variant	Intron 9 of 12	1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.146 AC: 17488 AN: 119730 Hom.: 1273 Cov.: 25

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.146 AC: 17486 AN: 119750 Hom.: 1273 Cov.: 25 AF XY: 0.150 AC XY: 8393 AN XY: 55958

African (AFR) AF: 0.197 AC: 6379 AN: 32326

American (AMR) AF: 0.213 AC: 2185 AN: 10276

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 532 AN: 3214

East Asian (EAS) AF: 0.0194 AC: 78 AN: 4020

South Asian (SAS) AF: 0.0823 AC: 304 AN: 3692

European-Finnish (FIN) AF: 0.146 AC: 628 AN: 4296

Middle Eastern (MID) AF: 0.228 AC: 37 AN: 162

European-Non Finnish (NFE) AF: 0.117 AC: 6949 AN: 59340

Other (OTH) AF: 0.178 AC: 286 AN: 1610

Alfa AF: 0.0369 Hom.: 38

Bravo AF: 0.129

Asia WGS AF: 0.0530 AC: 183 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.15
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: rs10515323; hg19: chr5-101583655;