rs7734060

Variant names:

• chr5-102444775-T-G
• rs7734060
• NM_173488.5:c.1132-6014A>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.1132-6014A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,138 control chromosomes in the GnomAD database, including 3,374 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 0.19 (3374 hom., cov: 32)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.1132-6014A>C		intron_variant	Intron 6 of 13	ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1132-6014A>C		intron_variant	Intron 6 of 13	1	NM_173488.5	ENSP00000421339.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28955 AN: 152020 Hom.: 3373 Cov.: 32

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.190 AC: 28957 AN: 152138 Hom.: 3374 Cov.: 32 AF XY: 0.192 AC XY: 14286 AN XY: 74340

African (AFR) AF: 0.0572 AC: 2378 AN: 41564

American (AMR) AF: 0.193 AC: 2955 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5178

South Asian (SAS) AF: 0.280 AC: 1346 AN: 4812

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10572

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17062 AN: 67954

Other (OTH) AF: 0.174 AC: 368 AN: 2116

Alfa AF: 0.225 Hom.: 4234

Bravo AF: 0.184

Asia WGS AF: 0.242 AC: 839 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.30
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: rs7734060; hg19: chr5-101780479; COSMIC: COSV65807577;