rs174414

Variant names:

• chr5-102257038-T-A
• rs174414
• NM_180991.5:c.1469+77A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-102257038-T-A
• chr5-102257038-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_180991.5(SLCO4C1):​c.1469+77A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000938 in 1,066,186 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 9.4e-7 (0 hom.)
• Consequence: SLCO4C1 NM_180991.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 8 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4C1	NM_180991.5	c.1469+77A>T		intron_variant	Intron 8 of 12	ENST00000310954.7	NP_851322.3
SLCO4C1	XM_011543370.3	c.1205+77A>T		intron_variant	Intron 7 of 11		XP_011541672.1
SLCO4C1	XM_011543372.2	c.1055+77A>T		intron_variant	Intron 10 of 14		XP_011541674.1
SLCO4C1	XM_047417146.1	c.1055+77A>T		intron_variant	Intron 10 of 14		XP_047273102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4C1	ENST00000310954.7	c.1469+77A>T		intron_variant	Intron 8 of 12	1	NM_180991.5	ENSP00000309741.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 9.38e-7 AC: 1 AN: 1066186 Hom.: 0 AF XY: 0.00000194 AC XY: 1 AN XY: 515428

African (AFR) AF: 0.00 AC: 0 AN: 22420

American (AMR) AF: 0.00 AC: 0 AN: 15570

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14894

East Asian (EAS) AF: 0.00 AC: 0 AN: 29696

South Asian (SAS) AF: 0.0000340 AC: 1 AN: 29454

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41514

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3818

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 865526

Other (OTH) AF: 0.00 AC: 0 AN: 43294

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.87

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: rs174414; hg19: chr5-101592742;