rs688878

Variant names:

• chr11-67572478-G-A
• rs688878

Your query was ambiguous. Multiple possible variants found:

• chr11-67572478-G-A
• chr11-67572478-G-C

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 0.895 in 152,182 control chromosomes in the GnomAD database, including 61,036 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 0.90 (61036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 14 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 (SAS) allele frequency at 95% confidence interval = 0.912 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: 0.895 AC: 136163 AN: 152064 Hom.: 61016 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.895 AC: 136238 AN: 152182 Hom.: 61036 Cov.: 32 AF XY: 0.893 AC XY: 66466 AN XY: 74398

African (AFR) AF: 0.871 AC: 36162 AN: 41516

American (AMR) AF: 0.894 AC: 13650 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4502 AN: 5166

South Asian (SAS) AF: 0.921 AC: 4449 AN: 4828

European-Finnish (FIN) AF: 0.838 AC: 8876 AN: 10592

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62420 AN: 68026

Other (OTH) AF: 0.902 AC: 1903 AN: 2110

Alfa AF: 0.913 Hom.: 117520

Bravo AF: 0.898

Asia WGS AF: 0.900 AC: 3132 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	1.3
DANN	Benign	0.11
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs688878; hg19: chr11-67339949;