rs2238341

chr15-92161801-A-Gchr15-92161801-A-T

Variant summary

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

The NM_013272.4(SLCO3A1):c.1754-955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 17,470 control chromosomes in the GnomAD database, including 4 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 0.065 (4 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.1754-955A>G		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.1754-955A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1754-955A>G		intron_variant		1	NM_013272.4	P1
	ENST00000561674.1	n.186-4560T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0648 AC: 1131 AN: 17448 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.00833

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.00430

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0714

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0647 AC: 1130 AN: 17470 Hom.: 4 Cov.: 0 AF XY: 0.0609 AC XY: 523 AN XY: 8588

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.00431

Gnomad4 SAS AF: 0.0613

Gnomad4 FIN AF: 0.0684

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0702

Alfa AF: 0.465 Hom.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.3
Dann	Benign	0.16

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: rs2238341; hg19: chr15-92705031; COSMIC: COSV59234466; COSMIC: COSV59234466;