11-69003359-T-C

Variant names:

• chr11-69003359-T-C
• rs1249579

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.992

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.981

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.097

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1249579; hg19: chr11-68770827;