2-226235982-G-T

Variant names:

• chr2-226235982-G-T
• rs2972146

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 0.721 in 151,598 control chromosomes in the GnomAD database, including 40,145 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 0.72 (40145 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 113 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.721 AC: 109242 AN: 151484 Hom.: 40085 Cov.: 30

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.721 AC: 109365 AN: 151598 Hom.: 40145 Cov.: 30 AF XY: 0.722 AC XY: 53417 AN XY: 74030

African (AFR) AF: 0.843 AC: 34885 AN: 41366

American (AMR) AF: 0.753 AC: 11483 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2471 AN: 3468

East Asian (EAS) AF: 0.927 AC: 4803 AN: 5180

South Asian (SAS) AF: 0.771 AC: 3697 AN: 4798

European-Finnish (FIN) AF: 0.629 AC: 6493 AN: 10318

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43376 AN: 67926

Other (OTH) AF: 0.705 AC: 1479 AN: 2098

Alfa AF: 0.673 Hom.: 106782

Bravo AF: 0.737

Asia WGS AF: 0.860 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.34
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2972146; hg19: chr2-227100698;