5-102477456-T-C

Variant names:

• chr5-102477456-T-C
• rs10041507
• NM_173488.5:c.802+220A>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.802+220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,932 control chromosomes in the GnomAD database, including 31,041 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 0.64 (31041 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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.802+220A>G		intron	N/A	NP_775759.3
	SLCO6A1	NM_001289002.2		c.802+220A>G		intron	N/A	NP_001275931.1
	SLCO6A1	NM_001289004.2		c.617-1663A>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.802+220A>G		intron	N/A	ENSP00000421339.1
	SLCO6A1	ENST00000379807.7	TSL:1	c.802+220A>G		intron	N/A	ENSP00000369135.3
	SLCO6A1	ENST00000389019.7	TSL:1	c.617-1663A>G		intron	N/A	ENSP00000373671.3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96764 AN: 151814 Hom.: 31019 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.637 AC: 96828 AN: 151932 Hom.: 31041 Cov.: 31 AF XY: 0.640 AC XY: 47539 AN XY: 74254

African (AFR) AF: 0.656 AC: 27200 AN: 41432

American (AMR) AF: 0.572 AC: 8715 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2359 AN: 5146

South Asian (SAS) AF: 0.594 AC: 2859 AN: 4814

European-Finnish (FIN) AF: 0.732 AC: 7733 AN: 10564

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43430 AN: 67946

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.652 Hom.: 4163

Bravo AF: 0.629

Asia WGS AF: 0.525 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.9
DANN	Benign	0.64
PhyloP100		1.1
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: rs10041507; hg19: chr5-101813160; COSMIC: COSV65807830;