11-63406212-T-G

Variant names:

• chr11-63406212-T-G
• rs7101446
• NM_080866.3:c.1074-285T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.91).
• 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 rank	MANE	Protein	UniProt
SLC22A9	NM_080866.3	c.1074-285T>G		intron_variant	Intron 6 of 9	ENST00000279178.4	NP_543142.2
SLC22A9	XM_017017159.3	c.1074-285T>G		intron_variant	Intron 6 of 7		XP_016872648.1
SLC22A9	XM_047426335.1	c.381-285T>G		intron_variant	Intron 4 of 7		XP_047282291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A9	ENST00000279178.4	c.1074-285T>G		intron_variant	Intron 6 of 9	1	NM_080866.3	ENSP00000279178.3
SLC22A9	ENST00000536333.5	n.*202-285T>G		intron_variant	Intron 5 of 6	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

African (AFR) AF: 0.228 AC: 9475 AN: 41472

American (AMR) AF: 0.282 AC: 4303 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3540 AN: 5172

South Asian (SAS) AF: 0.282 AC: 1358 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10598

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13483 AN: 67994

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.217 Hom.: 17039

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
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7101446; hg19: chr11-63173684;