11-72143449-C-G

Variant names:

• chr11-72143449-C-G
• rs555306

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 0.813 in 152,064 control chromosomes in the GnomAD database, including 51,043 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 0.81 (51043 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.879 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: 0.813 AC: 123517 AN: 151946 Hom.: 51000 Cov.: 30

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.813 AC: 123611 AN: 152064 Hom.: 51043 Cov.: 30 AF XY: 0.811 AC XY: 60297 AN XY: 74336

African (AFR) AF: 0.652 AC: 27015 AN: 41422

American (AMR) AF: 0.891 AC: 13621 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3472

East Asian (EAS) AF: 0.774 AC: 3990 AN: 5152

South Asian (SAS) AF: 0.828 AC: 3985 AN: 4810

European-Finnish (FIN) AF: 0.854 AC: 9044 AN: 10596

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60039 AN: 68010

Other (OTH) AF: 0.833 AC: 1759 AN: 2112

Alfa AF: 0.831 Hom.: 5834

Bravo AF: 0.809

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs555306; hg19: chr11-71854493;