rs2238341

Variant names:

• chr15-92161801-A-G
• rs2238341
• NM_013272.4:c.1754-955A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-92161801-A-G
• chr15-92161801-A-T

Variant summary

Our verdict is Benign. The variant received -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. 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
• Publications: 3 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]

ENSG00000260661 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1754-955A>G		intron_variant	Intron 9 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1754-955A>G		intron_variant	Intron 9 of 10		NP_001138516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1754-955A>G		intron_variant	Intron 9 of 9	1	NM_013272.4	ENSP00000320634.6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0488 AC: 202 AN: 4138

American (AMR) AF: 0.0583 AC: 84 AN: 1440

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 21 AN: 328

East Asian (EAS) AF: 0.00431 AC: 4 AN: 928

South Asian (SAS) AF: 0.0613 AC: 56 AN: 914

European-Finnish (FIN) AF: 0.0684 AC: 87 AN: 1272

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 56

European-Non Finnish (NFE) AF: 0.0819 AC: 659 AN: 8046

Other (OTH) AF: 0.0702 AC: 16 AN: 228

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
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

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