11-63371010-G-T

Variant names:

• chr11-63371010-G-T
• rs566456
• NM_080866.3:c.403-125G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_080866.3(SLC22A9):​c.403-125G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC22A9 NM_080866.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 12 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080866.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A9	NM_080866.3	MANE Select	c.403-125G>T		intron	N/A	NP_543142.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A9	ENST00000279178.4	TSL:1 MANE Select	c.403-125G>T		intron	N/A	ENSP00000279178.3	Q8IVM8-1
	SLC22A9	ENST00000536333.5	TSL:1	n.403-125G>T		intron	N/A	ENSP00000440206.1	Q8IVM8-2
	SLC22A9	ENST00000863025.1		c.403-125G>T		intron	N/A	ENSP00000533084.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 491016 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 257124

African (AFR) AF: 0.00 AC: 0 AN: 12572

American (AMR) AF: 0.00 AC: 0 AN: 17936

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13138

East Asian (EAS) AF: 0.00 AC: 0 AN: 29846

South Asian (SAS) AF: 0.00 AC: 0 AN: 40824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37356

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3588

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 308922

Other (OTH) AF: 0.00 AC: 0 AN: 26834

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.097
DANN	Benign	0.37
PhyloP100		-1.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs566456;

hg19: chr11-63138482;