chr11-62975583-C-T

Position:

• chr11-62975583-C-T

Variant summary

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

The ENST00000540654.5(SLC22A6):​c.*756+1601G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 152,216 control chromosomes in the GnomAD database, including 241 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 0.047 (241 hom., cov: 31)
• Consequence: SLC22A6 ENST00000540654.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0639 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+1601G>A		intron_variant, NMD_transcript_variant		5		ENSP00000445946

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7201 AN: 152098 Hom.: 242 Cov.: 31

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0473 AC: 7198 AN: 152216 Hom.: 241 Cov.: 31 AF XY: 0.0480 AC XY: 3573 AN XY: 74424

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.0399

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.0655

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0600 Hom.: 429

Bravo AF: 0.0419

Asia WGS AF: 0.0200 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs736342; hg19: chr11-62743055;