22-37779470-G-T

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 0.556 in 152,060 control chromosomes in the GnomAD database, including 24,197 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 0.56 (24197 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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: 0.556 AC: 84528 AN: 151942 Hom.: 24192 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.556 AC: 84570 AN: 152060 Hom.: 24197 Cov.: 33 AF XY: 0.555 AC XY: 41228 AN XY: 74294

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.562

Alfa AF: 0.593 Hom.: 16408

Bravo AF: 0.554

Asia WGS AF: 0.592 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.7
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756813; hg19: chr22-38175477;