rs6484249

Variant names:

• chr11-26760127-T-C
• rs6484249

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;