22-49310652-T-C

Variant names:

• chr22-49310652-T-C
• rs2858522

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 0.856 in 152,186 control chromosomes in the GnomAD database, including 56,092 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 0.86 (56092 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.856 AC: 130223 AN: 152068 Hom.: 56047 Cov.: 31

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.856 AC: 130325 AN: 152186 Hom.: 56092 Cov.: 31 AF XY: 0.857 AC XY: 63742 AN XY: 74388

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.861

Alfa AF: 0.837 Hom.: 50954

Bravo AF: 0.860

Asia WGS AF: 0.906 AC: 3154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0040
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858522; hg19: chr22-49706577;