5-102294992-T-G

Variant names:

• chr5-102294992-T-G
• rs841922
• NM_180991.5:c.355+916A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_180991.5(SLCO4C1):​c.355+916A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,140 control chromosomes in the GnomAD database, including 44,135 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 0.76 (44135 hom., cov: 32)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 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 = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.355+916A>C		intron_variant	Intron 1 of 12	ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.355+916A>C		intron_variant	Intron 1 of 11		XP_011541672.1
SLCO4C1	XM_011543372.2	c.-142-193A>C		intron_variant	Intron 2 of 14		XP_011541674.1
SLCO4C1	XM_047417146.1	c.-142-193A>C		intron_variant	Intron 2 of 14		XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.355+916A>C		intron_variant	Intron 1 of 12	1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115157 AN: 152022 Hom.: 44075 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.758 AC: 115274 AN: 152140 Hom.: 44135 Cov.: 32 AF XY: 0.757 AC XY: 56310 AN XY: 74374

African (AFR) AF: 0.881 AC: 36564 AN: 41508

American (AMR) AF: 0.746 AC: 11421 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3710 AN: 5170

South Asian (SAS) AF: 0.691 AC: 3331 AN: 4822

European-Finnish (FIN) AF: 0.753 AC: 7971 AN: 10582

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47403 AN: 67970

Other (OTH) AF: 0.769 AC: 1622 AN: 2108

Alfa AF: 0.657 Hom.: 2096

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		-0.33
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: rs841922; hg19: chr5-101630696;