rs4121881

Positions:

• chr11-63372021-A-G
• chr11-63372021-A-T

Variant summary

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

The NM_080866.3(SLC22A9):​c.506+783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,912 control chromosomes in the GnomAD database, including 24,975 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 0.57 (24975 hom., cov: 31)
• Consequence: SLC22A9 NM_080866.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A9	NM_080866.3	c.506+783A>G		intron_variant		ENST00000279178.4	NP_543142.2
SLC22A9	XM_017017159.3	c.506+783A>G		intron_variant			XP_016872648.1
SLC22A9	XM_047426335.1	c.-33+783A>G		intron_variant			XP_047282291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4	c.506+783A>G		intron_variant		1	NM_080866.3	ENSP00000279178	P1
SLC22A9	ENST00000536333.5	c.506+783A>G		intron_variant, NMD_transcript_variant		1		ENSP00000440206

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86598 AN: 151792 Hom.: 24980 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.570 AC: 86618 AN: 151912 Hom.: 24975 Cov.: 31 AF XY: 0.566 AC XY: 42034 AN XY: 74240

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.564

Alfa AF: 0.606 Hom.: 38317

Bravo AF: 0.569

Asia WGS AF: 0.473 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4121881; hg19: chr11-63139493;