rs10483111

Variant names:

• chr22-22348040-G-A
• rs10483111
• ENST00000440829.1:n.234G>A

Variant summary

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

The ENST00000440829.1(ENSG00000232515):​n.234G>A 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 0.0626 in 152,226 control chromosomes in the GnomAD database, including 702 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 0.063 (702 hom., cov: 32)
  • Exomes 𝑓: 0.016 (0 hom.)
• Consequence: ENSG00000232515 ENST00000440829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

Genes affected

ENSG00000232515 (HGNC:):

IGL (HGNC:5853):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGL		n.22348040G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232515	ENST00000440829.1	n.234G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9509 AN: 151990 Hom.: 699 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00868

Gnomad OTH AF: 0.0426

GnomAD4 exome AF: 0.0164 AC: 2 AN: 122 Hom.: 0 Cov.: 0 AF XY: 0.0102 AC XY: 1 AN XY: 98

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0192

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0627 AC: 9532 AN: 152104 Hom.: 702 Cov.: 32 AF XY: 0.0641 AC XY: 4764 AN XY: 74378

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.0729

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.00868

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0243 Hom.: 71

Bravo AF: 0.0639

Asia WGS AF: 0.0640 AC: 225 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483111; hg19: chr22-22702390;