11-86075245-A-G

Position:

• chr11-86075245-A-G

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 0.242 in 152,016 control chromosomes in the GnomAD database, including 4,912 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 0.24 (4912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.242 AC: 36699 AN: 151898 Hom.: 4903 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.242 AC: 36732 AN: 152016 Hom.: 4912 Cov.: 32 AF XY: 0.240 AC XY: 17847 AN XY: 74316

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0810

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.246

Alfa AF: 0.230 Hom.: 1757

Bravo AF: 0.235

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17159904; hg19: chr11-85786287;