rs566456

Positions:

• chr11-63371010-G-A
• chr11-63371010-G-C
• chr11-63371010-G-T

Variant summary

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

The NM_080866.3(SLC22A9):​c.403-125G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 641,576 control chromosomes in the GnomAD database, including 119,343 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 0.61 (28774 hom., cov: 32)
  • Exomes 𝑓: 0.60 (90569 hom.)
• Consequence: SLC22A9 NM_080866.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

SLC22A9 (HGNC:16261): (solute carrier family 22 member 9) Enables anion:anion antiporter activity; short-chain fatty acid transmembrane transporter activity; and sodium-independent organic anion transmembrane transporter activity. Involved in hormone transport; short-chain fatty acid import; and sodium-independent organic anion transport. Located in basolateral 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A9	NM_080866.3	c.403-125G>A		intron_variant		ENST00000279178.4	NP_543142.2
SLC22A9	XM_017017159.3	c.403-125G>A		intron_variant			XP_016872648.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4	c.403-125G>A		intron_variant		1	NM_080866.3	ENSP00000279178	P1
SLC22A9	ENST00000536333.5	c.403-125G>A		intron_variant, NMD_transcript_variant		1		ENSP00000440206

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93157 AN: 151880 Hom.: 28745 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.592

GnomAD4 exome AF: 0.603 AC: 294978 AN: 489576 Hom.: 90569 AF XY: 0.597 AC XY: 153118 AN XY: 256342

Gnomad4 AFR exome AF: 0.636

Gnomad4 AMR exome AF: 0.537

Gnomad4 ASJ exome AF: 0.471

Gnomad4 EAS exome AF: 0.408

Gnomad4 SAS exome AF: 0.471

Gnomad4 FIN exome AF: 0.634

Gnomad4 NFE exome AF: 0.644

Gnomad4 OTH exome AF: 0.603

GnomAD4 genome AF: 0.613 AC: 93238 AN: 152000 Hom.: 28774 Cov.: 32 AF XY: 0.608 AC XY: 45157 AN XY: 74298

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.590

Alfa AF: 0.627 Hom.: 39602

Bravo AF: 0.613

Asia WGS AF: 0.510 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.33

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: rs566456; hg19: chr11-63138482; COSMIC: COSV54170389; COSMIC: COSV54170389;