22-37779470-G-T

Variant names:

• chr22-37779470-G-T
• rs5756813

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;