22-46144361-ATTTTTT-ATTTTTTT

Variant names:

• chr22-46144361-A-AT
• rs135558
• ENST00000846710.1:n.329-3217_329-3216insA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000846710.1(ENSG00000310037):​n.329-3217_329-3216insA 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 0.29 (6360 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310037	ENST00000846710.1		n.329-3217_329-3216insA		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.311+1389_311+1390insA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 42356 AN: 143966 Hom.: 6354 Cov.: 0

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.227

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.294 AC: 42390 AN: 144014 Hom.: 6360 Cov.: 0 AF XY: 0.288 AC XY: 20077 AN XY: 69730

African (AFR) AF: 0.342 AC: 13413 AN: 39206

American (AMR) AF: 0.216 AC: 3119 AN: 14432

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 771 AN: 3368

East Asian (EAS) AF: 0.0851 AC: 414 AN: 4864

South Asian (SAS) AF: 0.210 AC: 937 AN: 4452

European-Finnish (FIN) AF: 0.265 AC: 2371 AN: 8934

Middle Eastern (MID) AF: 0.232 AC: 64 AN: 276

European-Non Finnish (NFE) AF: 0.309 AC: 20301 AN: 65630

Other (OTH) AF: 0.297 AC: 584 AN: 1966

Alfa AF: 0.160 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;