rs7734060

Positions:

• chr5-102444775-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506729.6(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 ENST00000506729.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.1132-6014A>C		intron_variant		ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1132-6014A>C		intron_variant		1	NM_173488.5	ENSP00000421339	P1

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

Gnomad4 AFR AF: 0.0572

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.174

Alfa AF: 0.234 Hom.: 3369

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7734060; hg19: chr5-101780479; COSMIC: COSV65807577;