11-39215482-A-G

Position:

• chr11-39215482-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 0.57 in 151,920 control chromosomes in the GnomAD database, including 25,691 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 0.57 (25691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.570 AC: 86587 AN: 151802 Hom.: 25671 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.570 AC: 86644 AN: 151920 Hom.: 25691 Cov.: 32 AF XY: 0.574 AC XY: 42595 AN XY: 74252

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.610

Alfa AF: 0.449 Hom.: 1280

Bravo AF: 0.574

Asia WGS AF: 0.695 AC: 2409 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035693; hg19: chr11-39237032;