15-92114143-T-C

Position:

• chr15-92114143-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.1010-6322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 151,932 control chromosomes in the GnomAD database, including 36,528 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 0.69 (36528 hom., cov: 31)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.1010-6322T>C		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.1010-6322T>C		intron_variant
SLCO3A1	NR_135775.2	n.937-6322T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1010-6322T>C		intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104531 AN: 151814 Hom.: 36500 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.688 AC: 104600 AN: 151932 Hom.: 36528 Cov.: 31 AF XY: 0.691 AC XY: 51322 AN XY: 74268

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.736

Alfa AF: 0.727 Hom.: 89342

Bravo AF: 0.689

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.39

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: rs207954; hg19: chr15-92657373;