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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373032	XR_938256.2	n.722-16245A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288106	ENST00000717626.1	n.409-16245A>G		intron_variant	Intron 2 of 4

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 v4.3

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;