rs621942

Positions:

• chr11-86072696-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.261 in 151,874 control chromosomes in the GnomAD database, including 5,425 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 0.26 (5425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39550 AN: 151754 Hom.: 5425 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.261 AC: 39572 AN: 151874 Hom.: 5425 Cov.: 32 AF XY: 0.258 AC XY: 19117 AN XY: 74226

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.257

Alfa AF: 0.268 Hom.: 539

Bravo AF: 0.270

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	10
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs621942; hg19: chr11-85783738;