chr2-218161896-G-A

Variant names:

• chr2-218161896-G-A
• rs1567868

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 0.88 in 150,830 control chromosomes in the GnomAD database, including 59,410 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 0.88 (59410 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.937 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: 0.880 AC: 132690 AN: 150714 Hom.: 59381 Cov.: 30

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.880 AC: 132771 AN: 150830 Hom.: 59410 Cov.: 30 AF XY: 0.879 AC XY: 64762 AN XY: 73694

African (AFR) AF: 0.747 AC: 30074 AN: 40264

American (AMR) AF: 0.872 AC: 13290 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3362 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4744 AN: 5144

South Asian (SAS) AF: 0.849 AC: 4085 AN: 4814

European-Finnish (FIN) AF: 0.942 AC: 9979 AN: 10590

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64154 AN: 68008

Other (OTH) AF: 0.909 AC: 1905 AN: 2096

Alfa AF: 0.879 Hom.: 8781

Bravo AF: 0.871

Asia WGS AF: 0.883 AC: 3073 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	0.39
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1567868; hg19: chr2-219026619;