chr11-92102935-C-G

Variant names:

• chr11-92102935-C-G
• rs752544

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 0.904 in 151,904 control chromosomes in the GnomAD database, including 63,673 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 (63673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 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: 0.904 AC: 137288 AN: 151786 Hom.: 63644 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.904 AC: 137371 AN: 151904 Hom.: 63673 Cov.: 31 AF XY: 0.907 AC XY: 67356 AN XY: 74236

African (AFR) AF: 0.678 AC: 28079 AN: 41434

American (AMR) AF: 0.961 AC: 14615 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3311 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5122 AN: 5122

South Asian (SAS) AF: 0.996 AC: 4807 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10623 AN: 10624

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

European-Non Finnish (NFE) AF: 0.997 AC: 67693 AN: 67904

Other (OTH) AF: 0.921 AC: 1948 AN: 2114

Alfa AF: 0.946 Hom.: 8061

Bravo AF: 0.891

Asia WGS AF: 0.978 AC: 3400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.41
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs752544; hg19: chr11-91836101;