chr11-20523658-G-A

Variant names:

• chr11-20523658-G-A
• rs7130880

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 0.956 in 152,278 control chromosomes in the GnomAD database, including 69,914 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 0.96 (69914 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.956 AC: 145429 AN: 152160 Hom.: 69873 Cov.: 31

Gnomad AFR AF: 0.943

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.956 AC: 145528 AN: 152278 Hom.: 69914 Cov.: 31 AF XY: 0.953 AC XY: 70941 AN XY: 74456

African (AFR) AF: 0.943 AC: 39162 AN: 41550

American (AMR) AF: 0.896 AC: 13700 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3429 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3313 AN: 5166

South Asian (SAS) AF: 0.972 AC: 4687 AN: 4824

European-Finnish (FIN) AF: 0.975 AC: 10341 AN: 10606

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67680 AN: 68044

Other (OTH) AF: 0.951 AC: 2011 AN: 2114

Alfa AF: 0.974 Hom.: 84215

Bravo AF: 0.943

Asia WGS AF: 0.845 AC: 2938 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs7130880; hg19: chr11-20545204;