22-43917969-A-G

Variant names:

• chr22-43917969-A-G
• rs929090

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 0.486 in 152,138 control chromosomes in the GnomAD database, including 18,125 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 0.49 (18125 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73828 AN: 152020 Hom.: 18100 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.486 AC: 73900 AN: 152138 Hom.: 18125 Cov.: 33 AF XY: 0.492 AC XY: 36611 AN XY: 74390

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.498

Alfa AF: 0.476 Hom.: 28128

Bravo AF: 0.487

Asia WGS AF: 0.551 AC: 1914 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs929090; hg19: chr22-44313849;