2-23299618-A-G

Variant names:

• chr2-23299618-A-G
• rs17675487

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 0.362 in 152,158 control chromosomes in the GnomAD database, including 10,694 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 0.36 (10694 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.362 AC: 55013 AN: 152038 Hom.: 10693 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.362 AC: 55006 AN: 152158 Hom.: 10694 Cov.: 33 AF XY: 0.365 AC XY: 27163 AN XY: 74388

African (AFR) AF: 0.227 AC: 9423 AN: 41526

American (AMR) AF: 0.436 AC: 6658 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3292 AN: 5160

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4820

European-Finnish (FIN) AF: 0.395 AC: 4184 AN: 10588

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26606 AN: 67992

Other (OTH) AF: 0.416 AC: 878 AN: 2112

Alfa AF: 0.334 Hom.: 2052

Bravo AF: 0.365

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.9
DANN	Benign	0.70
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs17675487; hg19: chr2-23522489;