5-102393538-A-G

Variant names:

• chr5-102393538-A-G
• rs1562961
• NM_173488.5:c.1815-2493T>C

Variant summary

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

The NM_173488.5(SLCO6A1):​c.1815-2493T>C 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 152,008 control chromosomes in the GnomAD database, including 30,993 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 (30993 hom., cov: 32)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.1815-2493T>C		intron_variant	Intron 10 of 13	ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1815-2493T>C		intron_variant	Intron 10 of 13	1	NM_173488.5	ENSP00000421339.1
SLCO6A1	ENST00000379807.7	c.1815-2493T>C		intron_variant	Intron 10 of 13	1		ENSP00000369135.3
SLCO6A1	ENST00000389019.7	c.1629-2493T>C		intron_variant	Intron 9 of 12	1		ENSP00000373671.3
SLCO6A1	ENST00000513675.1	c.1056-2493T>C		intron_variant	Intron 5 of 8	2		ENSP00000421990.1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96708 AN: 151888 Hom.: 30970 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.600

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: 96774 AN: 152008 Hom.: 30993 Cov.: 32 AF XY: 0.640 AC XY: 47513 AN XY: 74284

African (AFR) AF: 0.655 AC: 27139 AN: 41462

American (AMR) AF: 0.572 AC: 8718 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2434 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2363 AN: 5168

South Asian (SAS) AF: 0.593 AC: 2856 AN: 4814

European-Finnish (FIN) AF: 0.732 AC: 7736 AN: 10562

Middle Eastern (MID) AF: 0.586 AC: 170 AN: 290

European-Non Finnish (NFE) AF: 0.639 AC: 43434 AN: 67976

Other (OTH) AF: 0.616 AC: 1302 AN: 2114

Alfa AF: 0.625 Hom.: 11963

Bravo AF: 0.629

Asia WGS AF: 0.525 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		0.47
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: rs1562961; hg19: chr5-101729242; COSMIC: COSV65807138; COSMIC: COSV65807138;