rs2906066

Variant names:

• chr5-142200712-A-G
• rs2906066

Your query was ambiguous. Multiple possible variants found:

• chr5-142200712-A-G
• chr5-142200712-A-T

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 0.923 in 152,116 control chromosomes in the GnomAD database, including 64,955 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 0.92 (64955 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 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: 0.923 AC: 140295 AN: 151996 Hom.: 64888 Cov.: 30

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.923 AC: 140422 AN: 152116 Hom.: 64955 Cov.: 30 AF XY: 0.923 AC XY: 68595 AN XY: 74342

African (AFR) AF: 0.981 AC: 40706 AN: 41490

American (AMR) AF: 0.930 AC: 14213 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4800 AN: 5162

South Asian (SAS) AF: 0.890 AC: 4281 AN: 4808

European-Finnish (FIN) AF: 0.920 AC: 9743 AN: 10590

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60794 AN: 67992

Other (OTH) AF: 0.904 AC: 1908 AN: 2110

Alfa AF: 0.910 Hom.: 7833

Bravo AF: 0.928

Asia WGS AF: 0.936 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2906066; hg19: chr5-141580277;