chr2-133809754-A-G

Variant names:

• chr2-133809754-A-G
• rs11896627

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 0.385 in 151,202 control chromosomes in the GnomAD database, including 11,845 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 0.38 (11845 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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: 0.385 AC: 58154 AN: 151082 Hom.: 11830 Cov.: 28

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.385 AC: 58211 AN: 151202 Hom.: 11845 Cov.: 28 AF XY: 0.382 AC XY: 28191 AN XY: 73848

African (AFR) AF: 0.492 AC: 20222 AN: 41142

American (AMR) AF: 0.434 AC: 6615 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 684 AN: 3458

East Asian (EAS) AF: 0.191 AC: 979 AN: 5132

South Asian (SAS) AF: 0.249 AC: 1185 AN: 4766

European-Finnish (FIN) AF: 0.344 AC: 3560 AN: 10362

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23860 AN: 67814

Other (OTH) AF: 0.331 AC: 694 AN: 2098

Alfa AF: 0.338 Hom.: 9311

Bravo AF: 0.399

Asia WGS AF: 0.268 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs11896627; hg19: chr2-134567325;