rs738089

chr22-20418308-G-Achr22-20418308-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.676 in 148,002 control chromosomes in the GnomAD database, including 34,449 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 0.68 (34449 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.676 AC: 100036 AN: 147930 Hom.: 34437 Cov.: 25

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.676 AC: 100076 AN: 148002 Hom.: 34449 Cov.: 25 AF XY: 0.674 AC XY: 48482 AN XY: 71942

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.661

Alfa AF: 0.659 Hom.: 17119

Bravo AF: 0.665

Asia WGS AF: 0.511 AC: 1780 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	6.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738089; hg19: chr22-20772598;