11-62991327-C-G

Position:

• chr11-62991327-C-G

Variant summary

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

The ENST00000539841.1(SLC22A8):​n.5405G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,660 control chromosomes in the GnomAD database, including 15,325 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 0.44 (15323 hom., cov: 30)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: SLC22A8 ENST00000539841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

SLC22A8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62991327C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A8	ENST00000539841.1	n.5405G>C		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67286 AN: 151536 Hom.: 15285 Cov.: 30

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.433

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.444 AC: 67370 AN: 151654 Hom.: 15323 Cov.: 30 AF XY: 0.447 AC XY: 33133 AN XY: 74070

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.437

Alfa AF: 0.426 Hom.: 1769

Bravo AF: 0.430

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792367; hg19: chr11-62758799;