rs9620688

Variant names:

• chr22-27383161-G-A
• rs9620688
• ENST00000729519.1:n.350-3946C>T

Variant summary

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

The ENST00000729519.1(ENSG00000280445):​n.350-3946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,064 control chromosomes in the GnomAD database, including 5,694 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 0.27 (5694 hom., cov: 32)
• Consequence: ENSG00000280445 ENST00000729519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 publications found

Genes affected

ENSG00000280445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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
ENSG00000280445	ENST00000729519.1	n.350-3946C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40716 AN: 151946 Hom.: 5689 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.268 AC: 40750 AN: 152064 Hom.: 5694 Cov.: 32 AF XY: 0.259 AC XY: 19254 AN XY: 74316

African (AFR) AF: 0.287 AC: 11916 AN: 41492

American (AMR) AF: 0.190 AC: 2909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.0971 AC: 501 AN: 5158

South Asian (SAS) AF: 0.164 AC: 789 AN: 4820

European-Finnish (FIN) AF: 0.245 AC: 2580 AN: 10538

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20366 AN: 67986

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.285 Hom.: 23912

Bravo AF: 0.267

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.81
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9620688; hg19: chr22-27779122;