chr2-146028495-A-G

Variant names:

• chr2-146028495-A-G
• rs11681122

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 (1318 hom., cov: 7)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS2: High Homozygotes in GnomAd4 at 1318 gene

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: 0.241 AC: 11032 AN: 45782 Hom.: 1316 Cov.: 7

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.241 AC: 11027 AN: 45810 Hom.: 1318 Cov.: 7 AF XY: 0.244 AC XY: 5315 AN XY: 21754

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0528 AC: 882 AN: 16718

American (AMR) AF: 0.356 AC: 1344 AN: 3770

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 409 AN: 1102

East Asian (EAS) AF: 0.466 AC: 598 AN: 1284

South Asian (SAS) AF: 0.319 AC: 349 AN: 1094

European-Finnish (FIN) AF: 0.299 AC: 581 AN: 1946

Middle Eastern (MID) AF: 0.339 AC: 21 AN: 62

European-Non Finnish (NFE) AF: 0.345 AC: 6564 AN: 19016

Other (OTH) AF: 0.301 AC: 170 AN: 564

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.340 Hom.: 711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.39
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11681122; hg19: chr2-146786063;