2-222406292-C-T

Variant names:

• chr2-222406292-C-T
• rs724149

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 0.506 in 151,610 control chromosomes in the GnomAD database, including 20,112 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 0.51 (20112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76715 AN: 151492 Hom.: 20100 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.506 AC: 76751 AN: 151610 Hom.: 20112 Cov.: 31 AF XY: 0.507 AC XY: 37541 AN XY: 74072

African (AFR) AF: 0.375 AC: 15520 AN: 41350

American (AMR) AF: 0.658 AC: 9999 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2224 AN: 3456

East Asian (EAS) AF: 0.463 AC: 2387 AN: 5150

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4812

European-Finnish (FIN) AF: 0.530 AC: 5559 AN: 10494

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36920 AN: 67838

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.536 Hom.: 3037

Bravo AF: 0.513

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.26
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs724149; hg19: chr2-223271011;