5-102434022-C-T

Variant names:

• chr5-102434022-C-T
• rs6878284
• NM_173488.5:c.1276+4595G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173488.5(SLCO6A1):​c.1276+4595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,320 control chromosomes in the GnomAD database, including 30,780 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 (30780 hom., cov: 30)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 21 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	NM_173488.5	MANE Select	c.1276+4595G>A		intron	N/A	NP_775759.3
	SLCO6A1	NM_001289002.2		c.1276+4595G>A		intron	N/A	NP_001275931.1
	SLCO6A1	NM_001289004.2		c.1090+4595G>A		intron	N/A	NP_001275933.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO6A1	ENST00000506729.6	TSL:1 MANE Select	c.1276+4595G>A		intron	N/A	ENSP00000421339.1
	SLCO6A1	ENST00000379807.7	TSL:1	c.1276+4595G>A		intron	N/A	ENSP00000369135.3
	SLCO6A1	ENST00000389019.7	TSL:1	c.1090+4595G>A		intron	N/A	ENSP00000373671.3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96225 AN: 151204 Hom.: 30758 Cov.: 30

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.636 AC: 96289 AN: 151320 Hom.: 30780 Cov.: 30 AF XY: 0.639 AC XY: 47227 AN XY: 73906

African (AFR) AF: 0.656 AC: 27024 AN: 41220

American (AMR) AF: 0.570 AC: 8667 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2423 AN: 3458

East Asian (EAS) AF: 0.456 AC: 2335 AN: 5122

South Asian (SAS) AF: 0.593 AC: 2843 AN: 4796

European-Finnish (FIN) AF: 0.731 AC: 7632 AN: 10444

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43292 AN: 67790

Other (OTH) AF: 0.614 AC: 1285 AN: 2092

Alfa AF: 0.636 Hom.: 53999

Bravo AF: 0.629

Asia WGS AF: 0.525 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		-0.11
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: rs6878284; hg19: chr5-101769726; COSMIC: COSV65807455; COSMIC: COSV65807455;