15-92128494-TGGGATGGGGCAG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_013272.4(SLCO3A1):c.1512+23_1512+34del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 1,611,622 control chromosomes in the GnomAD database, including 1,146 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.052 (562 hom., cov: 31)
  • Exomes 𝑓: 0.010 (584 hom.)
• Consequence: SLCO3A1 NM_013272.4 splice_donor_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.479

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 -10 ACMG points.

• BP6: Variant 15-92128494-TGGGATGGGGCAG-T is Benign according to our data. Variant chr15-92128494-TGGGATGGGGCAG-T is described in ClinVar as [Benign]. Clinvar id is 774718.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.1512+23_1512+34del		splice_donor_region_variant, intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.1512+23_1512+34del		splice_donor_region_variant, intron_variant
SLCO3A1	NR_135775.2	n.1439+23_1439+34del		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1512+23_1512+34del		splice_donor_region_variant, intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.0515 AC: 7828 AN: 151944 Hom.: 557 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0123

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00612

Gnomad OTH AF: 0.0354

GnomAD3 exomes AF: 0.0170 AC: 4247 AN: 249232 Hom.: 241 AF XY: 0.0141 AC XY: 1903 AN XY: 134664

Gnomad AFR exome AF: 0.169

Gnomad AMR exome AF: 0.0100

Gnomad ASJ exome AF: 0.00120

Gnomad EAS exome AF: 0.000600

Gnomad SAS exome AF: 0.0138

Gnomad FIN exome AF: 0.00104

Gnomad NFE exome AF: 0.00595

Gnomad OTH exome AF: 0.00826

GnomAD4 exome AF: 0.0103 AC: 15013 AN: 1459560 Hom.: 584 AF XY: 0.00990 AC XY: 7187 AN XY: 725960

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.0112

Gnomad4 ASJ exome AF: 0.00184

Gnomad4 EAS exome AF: 0.000277

Gnomad4 SAS exome AF: 0.0136

Gnomad4 FIN exome AF: 0.00115

Gnomad4 NFE exome AF: 0.00587

Gnomad4 OTH exome AF: 0.0154

GnomAD4 genome AF: 0.0517 AC: 7867 AN: 152062 Hom.: 562 Cov.: 31 AF XY: 0.0503 AC XY: 3741 AN XY: 74310

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.000850

Gnomad4 NFE AF: 0.00612

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.00834 Hom.: 6

Bravo AF: 0.0589

Asia WGS AF: 0.0300 AC: 104 AN: 3478

EpiCase AF: 0.00601

EpiControl AF: 0.00661

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs75758067; hg19: chr15-92671724;