rs1081166

Variant names:

• chr22-12203070-A-C
• rs1081166
• ENST00000754819.1:n.371-16076A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000754819.1(ENSG00000298316):​n.371-16076A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.031 (0 hom., cov: 47)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000298316 ENST00000754819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 4 publications found

Genes affected

ENSG00000298316 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=6.962).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754819.1. 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
	ENSG00000298316	ENST00000754819.1		n.371-16076A>C		intron	N/A
	ENSG00000298316	ENST00000754820.1		n.578-2735A>C		intron	N/A
	ENSG00000298316	ENST00000754821.1		n.403-16076A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 3799 AN: 122106 Hom.: 0 Cov.: 47

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.0303

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.0755

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.0652

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0456

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0311 AC: 3802 AN: 122202 Hom.: 0 Cov.: 47 AF XY: 0.0320 AC XY: 1918 AN XY: 59964

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0435 AC: 1425 AN: 32746

American (AMR) AF: 0.0327 AC: 393 AN: 12002

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 87 AN: 2642

East Asian (EAS) AF: 0.0759 AC: 269 AN: 3542

South Asian (SAS) AF: 0.0344 AC: 131 AN: 3808

European-Finnish (FIN) AF: 0.0302 AC: 266 AN: 8814

Middle Eastern (MID) AF: 0.0701 AC: 15 AN: 214

European-Non Finnish (NFE) AF: 0.0200 AC: 1118 AN: 56024

Other (OTH) AF: 0.0451 AC: 76 AN: 1684

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0635 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	7.0
PhyloP100		0.16

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: rs1081166;