chr11-69003359-T-C

Variant names:

• chr11-69003359-T-C
• rs1249579

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 0.979 in 152,206 control chromosomes in the GnomAD database, including 73,036 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 0.98 (73036 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.72
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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: 0.979 AC: 148936 AN: 152088 Hom.: 72975 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.980

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

GnomAD4 genome AF: 0.979 AC: 149057 AN: 152206 Hom.: 73036 Cov.: 31 AF XY: 0.979 AC XY: 72854 AN XY: 74412

African (AFR) AF: 0.946 AC: 39277 AN: 41516

American (AMR) AF: 0.992 AC: 15168 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3441 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4665 AN: 5162

South Asian (SAS) AF: 0.980 AC: 4712 AN: 4808

European-Finnish (FIN) AF: 0.999 AC: 10605 AN: 10618

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67914 AN: 68020

Other (OTH) AF: 0.981 AC: 2076 AN: 2116

Alfa AF: 0.989 Hom.: 9239

Bravo AF: 0.977

Asia WGS AF: 0.939 AC: 3265 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	0.11
DANN	Benign	0.097
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1249579; hg19: chr11-68770827;