rs4121881

Variant names:

• chr11-63372021-A-G
• rs4121881
• NM_080866.3:c.506+783A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC22A9	NM_080866.3	c.506+783A>G		intron_variant	Intron 2 of 9	ENST00000279178.4	NP_543142.2
SLC22A9	XM_017017159.3	c.506+783A>G		intron_variant	Intron 2 of 7		XP_016872648.1
SLC22A9	XM_047426335.1	c.-33+783A>G		intron_variant	Intron 1 of 7		XP_047282291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4	c.506+783A>G		intron_variant	Intron 2 of 9	1	NM_080866.3	ENSP00000279178.3
SLC22A9	ENST00000536333.5	n.506+783A>G		intron_variant	Intron 2 of 6	1		ENSP00000440206.1

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

African (AFR) AF: 0.517 AC: 21407 AN: 41418

American (AMR) AF: 0.550 AC: 8385 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2232 AN: 5164

South Asian (SAS) AF: 0.449 AC: 2158 AN: 4808

European-Finnish (FIN) AF: 0.621 AC: 6547 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42173 AN: 67932

Other (OTH) AF: 0.564 AC: 1190 AN: 2110

Alfa AF: 0.602 Hom.: 52349

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
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4121881; hg19: chr11-63139493;