22-38904931-A-G

Variant names:

• chr22-38904931-A-G
• rs2413552
• ENST00000717626.1:n.409-16245A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717626.1(ENSG00000288106):​n.409-16245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,148 control chromosomes in the GnomAD database, including 39,531 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 0.71 (39531 hom., cov: 32)
• Consequence: ENSG00000288106 ENST00000717626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 3 publications found

Genes affected

ENSG00000288106 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717626.1. 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
	ENSG00000288106	ENST00000717626.1		n.409-16245A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107186 AN: 152030 Hom.: 39482 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.705 AC: 107283 AN: 152148 Hom.: 39531 Cov.: 32 AF XY: 0.702 AC XY: 52207 AN XY: 74382

African (AFR) AF: 0.923 AC: 38338 AN: 41524

American (AMR) AF: 0.523 AC: 7989 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4363 AN: 5182

South Asian (SAS) AF: 0.678 AC: 3270 AN: 4826

European-Finnish (FIN) AF: 0.611 AC: 6452 AN: 10562

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42388 AN: 67986

Other (OTH) AF: 0.677 AC: 1429 AN: 2112

Alfa AF: 0.645 Hom.: 16264

Bravo AF: 0.705

Asia WGS AF: 0.745 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.48
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2413552; hg19: chr22-39300936;