chr11-2116909-A-G

Variant names:

• chr11-2116909-A-G
• rs6578985

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 0.715 in 152,130 control chromosomes in the GnomAD database, including 39,110 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 0.71 (39110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108618 AN: 152012 Hom.: 39065 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.715 AC: 108724 AN: 152130 Hom.: 39110 Cov.: 33 AF XY: 0.711 AC XY: 52883 AN XY: 74346

African (AFR) AF: 0.744 AC: 30861 AN: 41502

American (AMR) AF: 0.767 AC: 11727 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2406 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2525 AN: 5168

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4820

European-Finnish (FIN) AF: 0.740 AC: 7823 AN: 10576

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48535 AN: 67982

Other (OTH) AF: 0.704 AC: 1487 AN: 2112

Alfa AF: 0.713 Hom.: 84853

Bravo AF: 0.722

Asia WGS AF: 0.534 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6578985; hg19: chr11-2138139;