22-30674506-C-T

Variant names:

• chr22-30674506-C-T
• rs5753271

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 0.118 in 151,974 control chromosomes in the GnomAD database, including 1,735 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 0.12 (1735 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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: 0.118 AC: 17861 AN: 151856 Hom.: 1730 Cov.: 31

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.118 AC: 17870 AN: 151974 Hom.: 1735 Cov.: 31 AF XY: 0.130 AC XY: 9619 AN XY: 74270

African (AFR) AF: 0.0255 AC: 1059 AN: 41478

American (AMR) AF: 0.163 AC: 2492 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5150

South Asian (SAS) AF: 0.282 AC: 1350 AN: 4790

European-Finnish (FIN) AF: 0.245 AC: 2584 AN: 10568

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7332 AN: 67936

Other (OTH) AF: 0.122 AC: 257 AN: 2106

Alfa AF: 0.113 Hom.: 3446

Bravo AF: 0.110

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs5753271; hg19: chr22-31070493;