22-46144361-ATTTTTT-ATTTTTTTT

Variant names:

• chr22-46144361-A-ATT
• rs135558
• ENST00000846710.1:n.329-3217_329-3216insAA

Variant summary

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

The ENST00000846710.1(ENSG00000310037):​n.329-3217_329-3216insAA 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 0.021 (94 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 = 0.0705 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
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.329-3217_329-3216insAA		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.311+1389_311+1390insAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3036 AN: 144124 Hom.: 95 Cov.: 0

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00894

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000205

Gnomad SAS AF: 0.000671

Gnomad FIN AF: 0.000223

Gnomad MID AF: 0.00662

Gnomad NFE AF: 0.000457

Gnomad OTH AF: 0.0112

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

GnomAD4 genome AF: 0.0211 AC: 3041 AN: 144172 Hom.: 94 Cov.: 0 AF XY: 0.0204 AC XY: 1426 AN XY: 69812

African (AFR) AF: 0.0727 AC: 2853 AN: 39238

American (AMR) AF: 0.00893 AC: 129 AN: 14446

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3370

East Asian (EAS) AF: 0.000205 AC: 1 AN: 4868

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

European-Finnish (FIN) AF: 0.000223 AC: 2 AN: 8964

Middle Eastern (MID) AF: 0.00719 AC: 2 AN: 278

European-Non Finnish (NFE) AF: 0.000457 AC: 30 AN: 65696

Other (OTH) AF: 0.0112 AC: 22 AN: 1968

Alfa AF: 0.000297 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;