chr5-102381668-A-C

Position:

• chr5-102381668-A-C

Variant summary

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

The NM_173488.5(SLCO6A1):​c.2017+7020T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 150,428 control chromosomes in the GnomAD database, including 29,974 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 0.63 (29974 hom., cov: 28)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.2017+7020T>G		intron_variant		ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.2017+7020T>G		intron_variant		1	NM_173488.5	ENSP00000421339	P1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 94554 AN: 150324 Hom.: 29955 Cov.: 28

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.629 AC: 94614 AN: 150428 Hom.: 29974 Cov.: 28 AF XY: 0.631 AC XY: 46284 AN XY: 73312

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.617

Alfa AF: 0.646 Hom.: 5276

Bravo AF: 0.619

Asia WGS AF: 0.524 AC: 1818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55

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: rs6873738; hg19: chr5-101717372; COSMIC: COSV65807071;