22-49240215-G-C

Variant names:

• chr22-49240215-G-C
• rs5770111

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.867 in 152,274 control chromosomes in the GnomAD database, including 57,319 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 0.87 (57319 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.867 AC: 131865 AN: 152156 Hom.: 57268 Cov.: 34

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.867 AC: 131976 AN: 152274 Hom.: 57319 Cov.: 34 AF XY: 0.864 AC XY: 64357 AN XY: 74462

African (AFR) AF: 0.903 AC: 37554 AN: 41572

American (AMR) AF: 0.884 AC: 13529 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2918 AN: 3470

East Asian (EAS) AF: 0.931 AC: 4823 AN: 5178

South Asian (SAS) AF: 0.800 AC: 3859 AN: 4822

European-Finnish (FIN) AF: 0.839 AC: 8889 AN: 10600

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57474 AN: 68010

Other (OTH) AF: 0.867 AC: 1831 AN: 2112

Alfa AF: 0.813 Hom.: 2457

Bravo AF: 0.873

Asia WGS AF: 0.879 AC: 3058 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	1.6
DANN	Benign	0.52
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs5770111; hg19: chr22-49636141;