5-102411004-G-T

Variant names:

• chr5-102411004-G-T
• rs1901521
• NM_173488.5:c.1626+1986C>A

Variant summary

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

The NM_173488.5(SLCO6A1):​c.1626+1986C>A 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 151,920 control chromosomes in the GnomAD database, including 31,002 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 (31002 hom., cov: 30)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.1626+1986C>A		intron_variant	Intron 9 of 13	ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1626+1986C>A		intron_variant	Intron 9 of 13	1	NM_173488.5	ENSP00000421339.1
SLCO6A1	ENST00000379807.7	c.1626+1986C>A		intron_variant	Intron 9 of 13	1		ENSP00000369135.3
SLCO6A1	ENST00000389019.7	c.1440+1986C>A		intron_variant	Intron 8 of 12	1		ENSP00000373671.3
SLCO6A1	ENST00000513675.1	c.867+1986C>A		intron_variant	Intron 4 of 8	2		ENSP00000421990.1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96700 AN: 151802 Hom.: 30980 Cov.: 30

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.456

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: 96764 AN: 151920 Hom.: 31002 Cov.: 30 AF XY: 0.640 AC XY: 47501 AN XY: 74220

African (AFR) AF: 0.656 AC: 27187 AN: 41444

American (AMR) AF: 0.572 AC: 8719 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2351 AN: 5154

South Asian (SAS) AF: 0.594 AC: 2853 AN: 4804

European-Finnish (FIN) AF: 0.732 AC: 7723 AN: 10546

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

European-Non Finnish (NFE) AF: 0.639 AC: 43402 AN: 67944

Other (OTH) AF: 0.615 AC: 1295 AN: 2104

Alfa AF: 0.632 Hom.: 50111

Bravo AF: 0.629

Asia WGS AF: 0.523 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.68
PhyloP100		-0.49
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: rs1901521; hg19: chr5-101746708; COSMIC: COSV65807246;