chr6-158519979-A-G

Variant names:

• chr6-158519979-A-G
• rs1866896

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 0.692 in 151,894 control chromosomes in the GnomAD database, including 38,017 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 0.69 (38017 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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: 0.692 AC: 104978 AN: 151776 Hom.: 37964 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.692 AC: 105082 AN: 151894 Hom.: 38017 Cov.: 30 AF XY: 0.693 AC XY: 51432 AN XY: 74244

African (AFR) AF: 0.913 AC: 37877 AN: 41466

American (AMR) AF: 0.552 AC: 8426 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1976 AN: 3462

East Asian (EAS) AF: 0.471 AC: 2417 AN: 5136

South Asian (SAS) AF: 0.650 AC: 3127 AN: 4810

European-Finnish (FIN) AF: 0.749 AC: 7905 AN: 10558

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.608 AC: 41291 AN: 67882

Other (OTH) AF: 0.627 AC: 1324 AN: 2112

Alfa AF: 0.627 Hom.: 128961

Bravo AF: 0.682

Asia WGS AF: 0.583 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1866896; hg19: chr6-158941011;