15-92128494-TGGGATGGGGCAG-T

Variant names:

• chr15-92128494-TGGGATGGGGCAG-T
• rs75758067
• NM_013272.4:c.1512+23_1512+34delGGGGCAGGGGAT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000318445.11(SLCO3A1):​c.1512+6_1512+17delGGGATGGGGCAG variant causes a splice 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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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 ENST00000318445.11 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.479
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000318445.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.1512+23_1512+34delGGGGCAGGGGAT		intron	N/A	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.1512+23_1512+34delGGGGCAGGGGAT		intron	N/A	NP_001138516.1	Q9UIG8-2
	SLCO3A1	NR_135775.2		n.1439+23_1439+34delGGGGCAGGGGAT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.1512+6_1512+17delGGGATGGGGCAG		splice_region intron	N/A	ENSP00000320634.6	Q9UIG8-1
	SLCO3A1	ENST00000424469.2	TSL:1	c.1512+6_1512+17delGGGATGGGGCAG		splice_region intron	N/A	ENSP00000387846.2	Q9UIG8-2
	SLCO3A1	ENST00000555769.5	TSL:1	n.1407+6_1407+17delGGGATGGGGCAG		splice_region intron	N/A

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

GnomAD2 exomes AF: 0.0170 AC: 4247 AN: 249232 AF XY: 0.0141

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 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

African (AFR) AF: 0.171 AC: 5709 AN: 33300

American (AMR) AF: 0.0112 AC: 499 AN: 44594

Ashkenazi Jewish (ASJ) AF: 0.00184 AC: 48 AN: 26064

East Asian (EAS) AF: 0.000277 AC: 11 AN: 39666

South Asian (SAS) AF: 0.0136 AC: 1172 AN: 86030

European-Finnish (FIN) AF: 0.00115 AC: 61 AN: 53026

Middle Eastern (MID) AF: 0.0111 AC: 64 AN: 5750

European-Non Finnish (NFE) AF: 0.00587 AC: 6523 AN: 1110864

Other (OTH) AF: 0.0154 AC: 926 AN: 60266

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

African (AFR) AF: 0.168 AC: 6949 AN: 41430

American (AMR) AF: 0.0216 AC: 330 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3472

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5158

South Asian (SAS) AF: 0.0123 AC: 59 AN: 4808

European-Finnish (FIN) AF: 0.000850 AC: 9 AN: 10588

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00612 AC: 416 AN: 67990

Other (OTH) AF: 0.0355 AC: 75 AN: 2110

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs75758067; hg19: chr15-92671724;