5-102374232-G-T

Variant names:

• chr5-102374232-G-T
• rs6877722
• NM_173488.5:c.2018-738C>A

Variant summary

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

The NM_173488.5(SLCO6A1):​c.2018-738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,944 control chromosomes in the GnomAD database, including 31,235 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 (31235 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5	c.2018-738C>A		intron_variant	Intron 12 of 13	ENST00000506729.6	NP_775759.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.2018-738C>A		intron_variant	Intron 12 of 13	1	NM_173488.5	ENSP00000421339.1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97041 AN: 151826 Hom.: 31212 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.639 AC: 97107 AN: 151944 Hom.: 31235 Cov.: 31 AF XY: 0.642 AC XY: 47678 AN XY: 74262

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.617

Alfa AF: 0.554 Hom.: 1585

Bravo AF: 0.632

Asia WGS AF: 0.527 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.42

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: rs6877722; hg19: chr5-101709936; COSMIC: COSV65807003; COSMIC: COSV65807003;