5-102388171-T-C

Variant names:

• chr5-102388171-T-C
• rs1901512
• NM_173488.5:c.2017+517A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173488.5(SLCO6A1):​c.2017+517A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,938 control chromosomes in the GnomAD database, including 32,505 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 0.65 (32505 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 5 publications found

Genes affected

SLCO6A1 (HGNC:23613): (solute carrier organic anion transporter family member 6A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173488.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	NM_173488.5	MANE Select	c.2017+517A>G		intron	N/A	NP_775759.3
	SLCO6A1	NM_001289002.2		c.2017+517A>G		intron	N/A	NP_001275931.1
	SLCO6A1	NM_001289004.2		c.1831+517A>G		intron	N/A	NP_001275933.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	ENST00000506729.6	TSL:1 MANE Select	c.2017+517A>G		intron	N/A	ENSP00000421339.1
	SLCO6A1	ENST00000379807.7	TSL:1	c.2017+517A>G		intron	N/A	ENSP00000369135.3
	SLCO6A1	ENST00000389019.7	TSL:1	c.1831+517A>G		intron	N/A	ENSP00000373671.3

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98854 AN: 151820 Hom.: 32486 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.651 AC: 98915 AN: 151938 Hom.: 32505 Cov.: 31 AF XY: 0.653 AC XY: 48474 AN XY: 74260

African (AFR) AF: 0.611 AC: 25305 AN: 41420

American (AMR) AF: 0.585 AC: 8941 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2494 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2353 AN: 5142

South Asian (SAS) AF: 0.609 AC: 2935 AN: 4822

European-Finnish (FIN) AF: 0.747 AC: 7875 AN: 10544

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46846 AN: 67950

Other (OTH) AF: 0.632 AC: 1335 AN: 2112

Alfa AF: 0.656 Hom.: 14069

Bravo AF: 0.641

Asia WGS AF: 0.531 AC: 1841 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.83
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1901512; hg19: chr5-101723875;