22-36273049-C-T

Variant names:

• chr22-36273049-C-T
• rs4821475

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 0.372 in 152,032 control chromosomes in the GnomAD database, including 12,015 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 0.37 (12015 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 10 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 = 0.688 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56426 AN: 151914 Hom.: 11971 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.372 AC: 56531 AN: 152032 Hom.: 12015 Cov.: 31 AF XY: 0.381 AC XY: 28333 AN XY: 74306

African (AFR) AF: 0.530 AC: 21977 AN: 41444

American (AMR) AF: 0.364 AC: 5566 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3662 AN: 5180

South Asian (SAS) AF: 0.551 AC: 2648 AN: 4806

European-Finnish (FIN) AF: 0.345 AC: 3648 AN: 10564

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17250 AN: 67980

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.305 Hom.: 7469

Bravo AF: 0.375

Asia WGS AF: 0.677 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.13
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4821475; hg19: chr22-36669095;