rs6484249

chr11-26760127-T-C

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 0.887 in 151,890 control chromosomes in the GnomAD database, including 59,865 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 0.89 (59865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134630 AN: 151772 Hom.: 59830 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.887 AC: 134723 AN: 151890 Hom.: 59865 Cov.: 32 AF XY: 0.885 AC XY: 65715 AN XY: 74236

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.897

Alfa AF: 0.887 Hom.: 15284

Bravo AF: 0.878

Asia WGS AF: 0.906 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.076
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6484249; hg19: chr11-26781674;