22-43917969-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;