rs10483111

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000232515 (HGNC:):

IGL (HGNC:5853):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.0192 AC: 2 AN: 104

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.177 AC: 7338 AN: 41484

American (AMR) AF: 0.0280 AC: 428 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3466

East Asian (EAS) AF: 0.0729 AC: 375 AN: 5146

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4808

European-Finnish (FIN) AF: 0.0554 AC: 587 AN: 10602

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.00868 AC: 590 AN: 67998

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0227 Hom.: 311

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10483111; hg19: chr22-22702390;