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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440829.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232515	ENST00000440829.1	TSL:6	n.234G>A		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10483111;

hg19: chr22-22702390;