11-63406212-T-G

Position:

• chr11-63406212-T-G

Variant summary

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

The NM_080866.3(SLC22A9):​c.1074-285T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,122 control chromosomes in the GnomAD database, including 4,723 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 0.23 (4723 hom., cov: 32)
• Consequence: SLC22A9 NM_080866.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A9	NM_080866.3	c.1074-285T>G		intron_variant		ENST00000279178.4	NP_543142.2
SLC22A9	XM_017017159.3	c.1074-285T>G		intron_variant			XP_016872648.1
SLC22A9	XM_047426335.1	c.381-285T>G		intron_variant			XP_047282291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4	c.1074-285T>G		intron_variant		1	NM_080866.3	ENSP00000279178.3
SLC22A9	ENST00000536333.5	n.*202-285T>G		intron_variant		1		ENSP00000440206.1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35054 AN: 152006 Hom.: 4709 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.231 AC: 35108 AN: 152122 Hom.: 4723 Cov.: 32 AF XY: 0.232 AC XY: 17220 AN XY: 74364

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.266

Alfa AF: 0.210 Hom.: 7337

Bravo AF: 0.243

Asia WGS AF: 0.481 AC: 1668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.53

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: rs7101446; hg19: chr11-63173684;