22-46144361-ATTTTTT-ATTTTT

Variant names:

• chr22-46144361-AT-A
• rs135558
• ENST00000846710.1:n.329-3217delA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000846710.1(ENSG00000310037):​n.329-3217delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0016 (0 hom., cov: 0)
• Consequence: ENSG00000310037 ENST00000846710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 1 publications found

Genes affected

ENSG00000310037 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310037	ENST00000846710.1		n.329-3217delA		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.311+1389delA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00158 AC: 228 AN: 143886 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000383

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00243

Gnomad ASJ AF: 0.000297

Gnomad EAS AF: 0.00102

Gnomad SAS AF: 0.000447

Gnomad FIN AF: 0.00766

Gnomad MID AF: 0.00331

Gnomad NFE AF: 0.00148

Gnomad OTH AF: 0.00204

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

GnomAD4 genome AF: 0.00160 AC: 230 AN: 143930 Hom.: 0 Cov.: 0 AF XY: 0.00192 AC XY: 134 AN XY: 69666

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

African (AFR) AF: 0.000433 AC: 17 AN: 39232

American (AMR) AF: 0.00243 AC: 35 AN: 14418

Ashkenazi Jewish (ASJ) AF: 0.000297 AC: 1 AN: 3366

East Asian (EAS) AF: 0.00103 AC: 5 AN: 4862

South Asian (SAS) AF: 0.000449 AC: 2 AN: 4454

European-Finnish (FIN) AF: 0.00766 AC: 68 AN: 8872

Middle Eastern (MID) AF: 0.00360 AC: 1 AN: 278

European-Non Finnish (NFE) AF: 0.00148 AC: 97 AN: 65590

Other (OTH) AF: 0.00203 AC: 4 AN: 1968

⚠️ 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: 0.00 Hom.: 318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs135558; hg19: chr22-46540236;