11-78091879-G-C

Variant names:

• chr11-78091879-G-C
• rs606164

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 0.855 in 152,106 control chromosomes in the GnomAD database, including 55,873 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 (55873 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 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 = 0.92 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: 0.854 AC: 129865 AN: 151988 Hom.: 55820 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.855 AC: 129977 AN: 152106 Hom.: 55873 Cov.: 31 AF XY: 0.851 AC XY: 63242 AN XY: 74352

African (AFR) AF: 0.928 AC: 38523 AN: 41534

American (AMR) AF: 0.756 AC: 11528 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3018 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3831 AN: 5154

South Asian (SAS) AF: 0.826 AC: 3981 AN: 4818

European-Finnish (FIN) AF: 0.837 AC: 8839 AN: 10566

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57561 AN: 68004

Other (OTH) AF: 0.853 AC: 1800 AN: 2110

Alfa AF: 0.823 Hom.: 2953

Bravo AF: 0.851

Asia WGS AF: 0.801 AC: 2781 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs606164; hg19: chr11-77802925;