chr5-102407922-T-G

Variant names:

• chr5-102407922-T-G
• rs1901522
• NM_173488.5:c.1626+5068A>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.1626+5068A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,946 control chromosomes in the GnomAD database, including 32,040 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 (32040 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	NM_173488.5	MANE Select	c.1626+5068A>C		intron	N/A	NP_775759.3
	SLCO6A1	NM_001289002.2		c.1626+5068A>C		intron	N/A	NP_001275931.1	Q86UG4-1
	SLCO6A1	NM_001289004.2		c.1440+5068A>C		intron	N/A	NP_001275933.1	Q86UG4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	ENST00000506729.6	TSL:1 MANE Select	c.1626+5068A>C		intron	N/A	ENSP00000421339.1	Q86UG4-1
	SLCO6A1	ENST00000379807.7	TSL:1	c.1626+5068A>C		intron	N/A	ENSP00000369135.3	Q86UG4-1
	SLCO6A1	ENST00000389019.7	TSL:1	c.1440+5068A>C		intron	N/A	ENSP00000373671.3	Q86UG4-2

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98287 AN: 151828 Hom.: 32017 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.647 AC: 98353 AN: 151946 Hom.: 32040 Cov.: 31 AF XY: 0.649 AC XY: 48210 AN XY: 74262

African (AFR) AF: 0.666 AC: 27588 AN: 41434

American (AMR) AF: 0.576 AC: 8799 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2349 AN: 5144

South Asian (SAS) AF: 0.595 AC: 2865 AN: 4814

European-Finnish (FIN) AF: 0.735 AC: 7771 AN: 10570

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

European-Non Finnish (NFE) AF: 0.654 AC: 44418 AN: 67938

Other (OTH) AF: 0.625 AC: 1314 AN: 2104

Alfa AF: 0.578 Hom.: 1815

Bravo AF: 0.640

Asia WGS AF: 0.527 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		1.1
Mutation Taster		=98/2	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: rs1901522; hg19: chr5-101743626; COSMIC: COSV65807228;