chr15-92019397-C-A

Position:

• chr15-92019397-C-A

Variant summary

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

The NM_013272.4(SLCO3A1):​c.647-75484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,046 control chromosomes in the GnomAD database, including 14,294 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 0.42 (14294 hom., cov: 33)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

Genes affected

SLCO3A1 (HGNC:10952): (solute carrier organic anion transporter family member 3A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in positive regulation of NF-kappaB transcription factor activity; positive regulation of protein phosphorylation; and prostaglandin transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.647-75484C>A		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.647-75484C>A		intron_variant
SLCO3A1	NR_135775.2	n.574-75484C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-75484C>A		intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64292 AN: 151928 Hom.: 14268 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.423 AC: 64377 AN: 152046 Hom.: 14294 Cov.: 33 AF XY: 0.432 AC XY: 32078 AN XY: 74306

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.408

Alfa AF: 0.362 Hom.: 12927

Bravo AF: 0.426

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.040
DANN	Benign	0.62

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: rs7171137; hg19: chr15-92562627;