rs10897310

Positions:

• chr11-62973704-T-C

Variant summary

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

The ENST00000540654.5(SLC22A6):​c.*756+3480A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,122 control chromosomes in the GnomAD database, including 7,315 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 0.30 (7315 hom., cov: 31)
• Consequence: SLC22A6 ENST00000540654.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

SLC22A6 (HGNC:10970): (solute carrier family 22 member 6) The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A6	ENST00000540654.5	c.*756+3480A>G		intron_variant, NMD_transcript_variant		5		ENSP00000445946

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45170 AN: 152004 Hom.: 7304 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.297 AC: 45213 AN: 152122 Hom.: 7315 Cov.: 31 AF XY: 0.297 AC XY: 22119 AN XY: 74352

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.315

Alfa AF: 0.326 Hom.: 3656

Bravo AF: 0.289

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10897310; hg19: chr11-62741176;