chr5-122086169-A-G

Variant names:

• chr5-122086169-A-G
• rs2979860

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 0.846 in 152,134 control chromosomes in the GnomAD database, including 54,750 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 0.85 (54750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128636 AN: 152016 Hom.: 54700 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.846 AC: 128740 AN: 152134 Hom.: 54750 Cov.: 32 AF XY: 0.848 AC XY: 63055 AN XY: 74360

African (AFR) AF: 0.921 AC: 38254 AN: 41546

American (AMR) AF: 0.832 AC: 12698 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2721 AN: 3466

East Asian (EAS) AF: 0.845 AC: 4382 AN: 5184

South Asian (SAS) AF: 0.852 AC: 4105 AN: 4818

European-Finnish (FIN) AF: 0.829 AC: 8779 AN: 10584

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54958 AN: 67958

Other (OTH) AF: 0.826 AC: 1742 AN: 2110

Alfa AF: 0.821 Hom.: 26097

Bravo AF: 0.846

Asia WGS AF: 0.885 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2979860; hg19: chr5-121421864;