chr2-179290436-A-G

Variant names:

• chr2-179290436-A-G
• rs16866688

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 0.175 in 152,248 control chromosomes in the GnomAD database, including 5,756 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 0.17 (5756 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26546 AN: 152130 Hom.: 5742 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.175 AC: 26604 AN: 152248 Hom.: 5756 Cov.: 33 AF XY: 0.169 AC XY: 12602 AN XY: 74470

African (AFR) AF: 0.515 AC: 21382 AN: 41496

American (AMR) AF: 0.0932 AC: 1425 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5190

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4828

European-Finnish (FIN) AF: 0.0102 AC: 108 AN: 10622

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3038 AN: 68028

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.135 Hom.: 641

Bravo AF: 0.196

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.69
DANN	Benign	0.85
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs16866688; hg19: chr2-180155163;