2-146136722-G-C

Variant names:

• chr2-146136722-G-C
• rs222808

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 0.243 in 152,022 control chromosomes in the GnomAD database, including 6,680 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 0.24 (6680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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: 0.243 AC: 36847 AN: 151904 Hom.: 6675 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.243 AC: 36896 AN: 152022 Hom.: 6680 Cov.: 32 AF XY: 0.237 AC XY: 17574 AN XY: 74296

African (AFR) AF: 0.514 AC: 21287 AN: 41406

American (AMR) AF: 0.149 AC: 2281 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3470

East Asian (EAS) AF: 0.149 AC: 769 AN: 5160

South Asian (SAS) AF: 0.169 AC: 815 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1220 AN: 10590

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9165 AN: 67988

Other (OTH) AF: 0.247 AC: 523 AN: 2114

Alfa AF: 0.0665 Hom.: 68

Bravo AF: 0.256

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.18
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs222808; hg19: chr2-146894290;