chr15-92142548-T-C

Position:

• chr15-92142548-T-C

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1513-4436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,026 control chromosomes in the GnomAD database, including 19,684 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 (19684 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.1513-4436T>C		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.1513-4436T>C		intron_variant
SLCO3A1	NR_135775.2	n.1440-4436T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1513-4436T>C		intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74501 AN: 151908 Hom.: 19646 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.491 AC: 74586 AN: 152026 Hom.: 19684 Cov.: 32 AF XY: 0.487 AC XY: 36193 AN XY: 74304

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.453

Alfa AF: 0.407 Hom.: 14063

Bravo AF: 0.514

Asia WGS AF: 0.463 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.46

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: rs2238355; hg19: chr15-92685778;