chr5-102434022-C-T

Position:

• chr5-102434022-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO6A1	NM_173488.5	c.1276+4595G>A		intron_variant		ENST00000506729.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1276+4595G>A		intron_variant		1	NM_173488.5	P1

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

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.614

Alfa AF: 0.645 Hom.: 4032

Bravo AF: 0.629

Asia WGS AF: 0.525 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.79

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: rs6878284; hg19: chr5-101769726; COSMIC: COSV65807455; COSMIC: COSV65807455;