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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.902

Alfa AF: 0.915 Hom.: 84792

Bravo AF: 0.898

Asia WGS AF: 0.900 AC: 3132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs688878; hg19: chr11-67339949;