11-86073937-A-C

Position:

• chr11-86073937-A-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 0.384 in 152,070 control chromosomes in the GnomAD database, including 11,449 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 0.38 (11449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.384 AC: 58420 AN: 151952 Hom.: 11444 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.384 AC: 58447 AN: 152070 Hom.: 11449 Cov.: 32 AF XY: 0.382 AC XY: 28410 AN XY: 74364

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.367

Alfa AF: 0.391 Hom.: 1089

Bravo AF: 0.392

Asia WGS AF: 0.446 AC: 1553 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	0.45
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638509; hg19: chr11-85784979;