22-30283398-A-G

Variant names:

• chr22-30283398-A-G
• rs2108093
• ENST00000827109.1:n.122+832T>C

Variant summary

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

The ENST00000827109.1(ENSG00000307561):​n.122+832T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,090 control chromosomes in the GnomAD database, including 58,581 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 0.87 (58581 hom., cov: 30)
• Consequence: ENSG00000307561 ENST00000827109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 8 publications found

Genes affected

ENSG00000307561 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307561	ENST00000827109.1	n.122+832T>C		intron_variant	Intron 1 of 1
ENSG00000307561	ENST00000827110.1	n.134+832T>C		intron_variant	Intron 1 of 2
ENSG00000307561	ENST00000827111.1	n.132-716T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132958 AN: 151972 Hom.: 58522 Cov.: 30

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.875 AC: 133074 AN: 152090 Hom.: 58581 Cov.: 30 AF XY: 0.880 AC XY: 65425 AN XY: 74346

African (AFR) AF: 0.967 AC: 40131 AN: 41506

American (AMR) AF: 0.870 AC: 13308 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3098 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4653 AN: 5142

South Asian (SAS) AF: 0.915 AC: 4415 AN: 4826

European-Finnish (FIN) AF: 0.887 AC: 9400 AN: 10594

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55272 AN: 67948

Other (OTH) AF: 0.879 AC: 1857 AN: 2112

Alfa AF: 0.832 Hom.: 223930

Bravo AF: 0.875

Asia WGS AF: 0.921 AC: 3203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2108093; hg19: chr22-30679387;