rs6873738

Variant names:

• chr5-102381668-A-C
• rs6873738
• NM_173488.5:c.2017+7020T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-102381668-A-C
• chr5-102381668-A-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+7020T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 150,428 control chromosomes in the GnomAD database, including 29,974 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 0.63 (29974 hom., cov: 28)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 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+7020T>G		intron	N/A	NP_775759.3
	SLCO6A1	NM_001289002.2		c.2017+7020T>G		intron	N/A	NP_001275931.1
	SLCO6A1	NM_001289004.2		c.1831+7020T>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+7020T>G		intron	N/A	ENSP00000421339.1
	SLCO6A1	ENST00000379807.7	TSL:1	c.2017+7020T>G		intron	N/A	ENSP00000369135.3
	SLCO6A1	ENST00000389019.7	TSL:1	c.1831+7020T>G		intron	N/A	ENSP00000373671.3

Frequencies

GnomAD3 genomes AF: 0.629 AC: 94554 AN: 150324 Hom.: 29955 Cov.: 28

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.629 AC: 94614 AN: 150428 Hom.: 29974 Cov.: 28 AF XY: 0.631 AC XY: 46284 AN XY: 73312

African (AFR) AF: 0.604 AC: 24790 AN: 41076

American (AMR) AF: 0.568 AC: 8574 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2435 AN: 3450

East Asian (EAS) AF: 0.457 AC: 2336 AN: 5108

South Asian (SAS) AF: 0.595 AC: 2860 AN: 4804

European-Finnish (FIN) AF: 0.735 AC: 7500 AN: 10204

Middle Eastern (MID) AF: 0.587 AC: 169 AN: 288

European-Non Finnish (NFE) AF: 0.653 AC: 44032 AN: 67410

Other (OTH) AF: 0.617 AC: 1291 AN: 2092

Alfa AF: 0.646 Hom.: 7031

Bravo AF: 0.619

Asia WGS AF: 0.524 AC: 1818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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: rs6873738; hg19: chr5-101717372; COSMIC: COSV65807071;